ProteinID Organism Length of noncoding sequence
16331117 Synechocystis 181
15618801 Chlamydolpha pneumoniae 1077
15645855 Helicobacter Pylori 1107
15673706 Lactococcus 266
I followed almost the same procedure outlined in the hand
out. Selecting the COGID was not very frustrating. I had to try around
5 COGIDs before getting to the above set of proteins.
The protein sequence (Amino Acid sequences) for above proteins are
>sll0362
MTTTPPVLSGPEIRQQFLNFFADRQHQILPSASLVPEDPTVLLTIAGMLPFKPIFLGQKSAEFPRATTSQ
KCIRTNDIENVGRTARHHTFFEMLGNFSFGDYFKSQAIAWAWELSTQVFKLPAERLVVSVFEEDDEAFAI
WRDEIGIPAHRIQRMGADDNFWVSGPTGPCGPCSEIYYDFHPELGDEKLDLEDDSRFIEFYNLVFMQYNR
DNAGNLTPLEKKNIDTGMGLERMAQILQKVPNNYETDLIFPIIQTAANIAGIDYAQANEKTKVSLKVIGD
HVRSVVHMIADGISASNLGRGYVLRRLIRRVVRHGRLLGINGEFTTKVAATAVQLAQPVYPNVLERQSLI
EQELQREEAAFLKTLERGEKLLADLMADGVTEIAGADAFTLYDTFGFPLELTQEIAEEQGITVDVEGFEK
AMQEQQERSKAAHETIDLTVQESLDKLANHIHPTEFLGYTDLQSSAIVKAVLVGGELVDQAVAGQTVQIV
LDQTPFYGESGGQIGDKGFLNGDNLLIRIEDVKRESGIFIHFGRVERGTVQIGTTITATIDRACRRRAQA
NHTATHLLQSALKRVVDEGISQAGSLVDFNRLRFDFNSPRAVTMEELQQIEDLINQWIAEAHQTEVAVMP
IADAKAKGAIAMFGEKYGAEVRVIDVPGVSLELCGGTHVANTAEIGLFKIVAETGIAAGVRRIEAVAGPS
VLDYLNVREAVVKELGDRLKAKPEEIPDRVHQLQQELKASQKQLEALKQELALQKSEQLLTQAQTVGEFK
ILVADLGTVDGESLKTAAERLQQKLGESAVVLASIPEEGKVSLVAAFSPQLVKTKQLKAGQFIGAIAKIC
GGGGGGRPNLAQAGGRDASKLPEALATAKQTLLAELG
>CPn0892
MLSNTIRSNFLKFYANRHHTILPSSPVFPHNDPSILFTNAGMNQFKDIFLNKEKVSYSRATTSQKCIRAG
GKHNDLDNVGHTSRHLTFFEMLGNFSFGDYFKAEAIAFAWEVSLSVFNFNPEGIYATVHEKDDEAFALWE
AYLPTDRIFRLTDKDNFWSMANTGPCGYCSELLFDRGPSFGNASSPLDDTDGERFLEYWNLVFMEFNRTS
EGSLLALPNKHVDTGAGLERLVSLIAGTHTVFEADVLRELIAKTEQLSGKVYHPDDSGAAFRVIADHVRS
LSFAIADGLLPGNTERGYVLRKILRRSVNYGRRLGFRNPFLAEIVPSLADAMGEAYPELKNSLSQIQKVL
TLEEESFFKTLDRGGNLLQQVLKSSSSSSCISGEDAFKLKDTYGMPIDEISLLAKDYDYSVDMDTFHKLE
QEAKERSRKNVVQSQGTSESIYNELHLTSEFIGYDHLSCDTFIEAIISKDHIVSSLQEKQEGAIVLKVSP
FYAEKGGQVGDSGEIFCSEGTFIVTHTTSPKAGLIVHHGRISQGSLTVEAAVTAQVNRYRRKRIANNHTA
CHLLHKALEITLGDHIRQAGSYVDDTKIRLDFTHPQAISPEDLLCIETLVNESIRENEPVDIREALYSDV
MNSSEIKQFFGDKYSDVVRVVSAGHSHELCGGTHAEATGDIGFFRITKEHAVAMGIRRIEAVTGEKAEAT
VHQQSEVLEEIATLLQVPRDQIVSRLTATLDERKQQDKRLNELENSLIQTKLDKLIHNCHQRQGITCLVH
HLAEHENHRLQQYAQCLHQRIPEKLISLWTTEKNGKYIVLSRVSDDLITQGVHAQDLLKAVLTPCGGRWG
GKDQSAQGSAPALPATEVLNETLWQWISTQLI
>HP1241
MDIRNEFLQFFQNKGHAVYPSMPLVPNDATLLFTNAGMVQFKDIFTGIVPRPSIPRAASSQLCMRAGGKH
NDLENVGYTARHHTLFEMLGNFSFGDYFKEEAILFAWEFVTKNLGFKPKDLYISVHEKDDEAVKLWEKFV
PVDRIKKMGDKDNFWQMGDSGPCGPCSEIYIDQGEKHFKGSEDYFGGEGDRFLEIWNLVFMQYERSNDGV
LSPLPKPSIDTGMGLERVQALLEHKLNNFDSSLFAPLMEEISELTSLDYASEFQPSFRVVADHARAVAFL
LAQGVHFNKEGRGYVLRRILRRALRHGYLMGLKEAFLYKVVGVVCEQFANTHAYLKESKEMVVKECFEEE
EHFLETLESGMELFNLSLKHLNENKIFDGKIAFKLYDTFGFPLDLTNDMLRSHGACADMQGFELCMQEQV
KRSKASWKGKQNNADFSAILNAYAPNVFVGYETTECSAKVLGFFDSDFKEITDANPNQEVWVLLEKTPFY
AEGGGAIGDRGALFKDNGEVAIVLDTKNFFGLNFSLLEIKKALKKGDQVIAQVSDERFEIAKHHSATHLL
QSALREVLGSHVSQAGSLVESKRLRFDFSHAKALNDEELEKVEDLVNAQIFKHLNSQVEHMPLNQAKDKG
ALALFSEKYAENVRVVSFKEASIELCGGIHVENTGLIGGFRIVKESGVSSGVRRIEAVCGKAFYQLAKEE
NKELKNAKTLLKNNDVIAGINKLKESVKNSQKAPVSMDLPVEKIHGVNLVVGVVEQGDIKEMIDRLKSKH
ERLLAMVFKKENERITLACGVKNAPIKANVWANEVAQILGGKGGGRGDFASAGGKDIENLQAALNLAKNT
ALKALEG
>L0343
MKTMTSAEVRQMFLDFFKSKGHTVEPSQSLVPVNDPTLLWINSGVATLKKYFDGSVVPENPRLTNAQKAI
RTNDIENVGKTARHHTMFEMLGNFSIGDYFRKEAIAFAWELLTSSEWFEFPAEKLYITYYPADKDTYNRW
VEVGVDPTHLVPIEDNFWEIGAGPSGPDTEIFFDRGEVYDPEHVGLKLLAEDIENDRYIEIWNIVLSQFN
ADPSIPRSEYPELPQKNIDTGMGLERMVCIIQGGKTNFDTDLFLPIIREIEKLSGKTYSPDSENMSFKVI
ADHIRSLSFAIGDGALPGNEGRGYVLRRLLRRAVMHGKKLGIQGKFLASLVPTVGKIMQSYYPEVLEKED
FIMQIIDREEETFNRTIDAGQKLIDELLLNLKSEGKDRLEGADIFRLYDTYGFPVELTEELAEDEGFKID
HEGFKVAMKAQQERARAAVVKGGSMGAQNETLSSIEVESEFLYEDKTTQGKLLVSIQDDEIVDEVSGKAQ
LVFDVTPFYAEMGGQVADHGVIKDAEGQVVANVLDVQHAPHGQNLHSVETLSPLKVGESYTLEIDKERRA
AVVKNHTATHLLHAALHNIVGNHALQAGSLNEVEFLRFDFTHFAQVTKEELAEIERQVNEVIWQSLKVET
VETDIATAKEMGAMALFGEKYGKNVRVVKIGDYSIELCGGTHTQTTSEIGLFKIVKEEGIGSGVRRIIAV
TGQKAYEAFKDAENTLNEVATMVKAPQTSQVLAKVTSLQDELKTAQKENDALAGKLAASQSDEIFKNVQT
AGSLNFIASEVTVPDANGLRNLADIWKQKELSDVLVLVAKIGEKVSLLVASKSSDVKAGNLVKELAPFVD
GRGGGKPDMAMAGGSKAAGIPELLAAVAEKLA
CLUSTAL W (1.81) Multiple Sequence Alignments
Sequence format is Pearson
Sequence 1: sll0362 877 aa
Sequence 2: CPn0892 872 aa
Sequence 3: HP1241 847 aa
Sequence 4: L0343 872 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 33.3716
Sequences (1:3) Aligned. Score: 34.2385
Sequences (1:4) Aligned. Score: 36.2385
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 32.4675
Sequences (2:4) Aligned. Score: 30.5046
Sequences (3:2) Aligned. Score: 32.1133
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 30.1063
Sequences (4:2) Aligned. Score: 30.5046
Sequences (4:3) Aligned. Score: 30.1063
Sequences (4:4) Aligned. Score: 100
Start of Multiple Alignment
There are 3 groups
Aligning...
Group 1: Sequences: 2 Score:12780
Group 2: Sequences: 3 Score:9601
Group 3: Sequences: 4 Score:9700
Alignment Score 10381
-------------------------------------------------------------------------------- Clustal output
CLUSTAL W (1.81) multiple sequence alignment
sll0362 MTTTPPVLSGPEIRQQFLNFFADRQHQILPSASLVPE-DPTVLLTIAGMLPFKPIFLGQK
L0343 MKT----MTSAEVRQMFLDFFKSKGHTVEPSQSLVPVNDPTLLWINSGVATLKKYFDGSV
HP1241 ----------MDIRNEFLQFFQNKGHAVYPSMPLVPN-DATLLFTNAGMVQFKDIFTGIV
CPn0892 -------MLSNTIRSNFLKFYANRHHTILPSSPVFPHNDPSILFTNAGMNQFKDIFLNKE
:*. **.*: .: * : ** .:.* *.::* :*: :* * .
sll0362 S-AEFPRATTSQKCIRT----NDIENVGRTARHHTFFEMLGNFSFGDYFKSQAIAWAWEL
L0343 V-PENPRLTNAQKAIRT----NDIENVGKTARHHTMFEMLGNFSIGDYFRKEAIAFAWEL
HP1241 PRPSIPRAASSQLCMRAGGKHNDLENVGYTARHHTLFEMLGNFSFGDYFKEEAILFAWEF
CPn0892 K-VSYSRATTSQKCIRAGGKHNDLDNVGHTSRHLTFFEMLGNFSFGDYFKAEAIAFAWEV
. .* :.:* .:*: **::*** *:** *:********:****: :** :***.
sll0362 ST--QVFKLPAERLVVSVFEEDDEAFAIWRDEIGIPAHRIQRMGADDNFWVSGPTGPCGP
L0343 LTSSEWFEFPAEKLYITYYPADKDTYNRWVEVGVDPTHLVP---IEDNFWEIG-AGPSGP
HP1241 VT--KNLGFKPKDLYISVHEKDDEAVKLWEKF--VPVDRIKKMGDKDNFWQMGDSGPCGP
CPn0892 SLS--VFNFNPEGIYATVHEKDDEAFALWEAY--LPTDRIFRLTDKDNFWSMANTGPCGY
: : .: : : . *.:: * *.. : .**** . :**.*
sll0362 CSEIYYD----FHPELGDEKLDLE--DDSRFIEFYNLVFMQYNRD---NAGNLTPLEKKN
L0343 DTEIFFDRGEVYDPEHVGLKLLAEDIENDRYIEIWNIVLSQFNADPSIPRSEYPELPQKN
HP1241 CSEIYID----QGEKHFKGSEDYFGGEGDRFLEIWNLVFMQYERS---NDGVLSPLPKPS
CPn0892 CSELLFD----RGPSFGNASSPLDDTDGERFLEYWNLVFMEFNRT---SEGSLLALPNKH
:*: * . . :..*::* :*:*: ::: . * :
sll0362 IDTGMGLERMAQILQKVPNNYETDLIFPIIQTAANIAGIDYAQANEKTKVSLKVIGDHVR
L0343 IDTGMGLERMVCIIQGGKTNFDTDLFLPIIREIEKLSGKTYSPDSEN--MSFKVIADHIR
HP1241 IDTGMGLERVQALLEHKLNNFDSSLFAPLMEEISELTSLDYASEFQP---SFRVVADHAR
CPn0892 VDTGAGLERLVSLIAGTHTVFEADVLRELIAKTEQLSGKVYHPDDSG--AAFRVIADHVR
:*** ****: :: . :::.:: :: :::. * . :::*:.** *
sll0362 SVVHMIADGISASNLGRGYVLRRLIRRVVRHGRLLGINGEFTTKVAATAVQLAQPVYPNV
L0343 SLSFAIGDGALPGNEGRGYVLRRLLRRAVMHGKKLGIQGKFLASLVPTVGKIMQSYYPEV
HP1241 AVAFLLAQGVHFNKEGRGYVLRRILRRALRHGYLMGLKEAFLYKVVGVVCEQFANTHAYL
CPn0892 SLSFAIADGLLPGNTERGYVLRKILRRSVNYGRRLGFRNPFLAEIVPSLADAMGEAYPEL
:: . :.:* .: ******:::** : :* :*:. * .:. . :. :
sll0362 LERQSLIEQELQREEAAFLKTLERGEKLLADLMA----DGVTEIAGADAFTLYDTFGFPL
L0343 LEKEDFIMQIIDREEETFNRTIDAGQKLIDELLLNLKSEGKDRLEGADIFRLYDTYGFPV
HP1241 KESKEMVVKECFEEEEHFLETLESGMELFNLSLKHLN--ENKIFDGKIAFKLYDTFGFPL
CPn0892 KNSLSQIQKVLTLEEESFFKTLDRGGNLLQQVLKSSS--SSSCISGEDAFKLKDTYGMPI
: . : : ** * .*:: * :*: : : * * * **:*:*:
sll0362 ELTQEIAEEQGITVDVEGFEKAMQEQQERSKAAHETIDLTVQESLDKLANHIHPTEFLGY
L0343 ELTEELAEDEGFKIDHEGFKVAMKAQQERARAAVVKGG-SMGAQNETLSSIEVESEFL-Y
HP1241 DLTNDMLRSHGACADMQGFELCMQEQVKRSKASWKGKQ--NNADFSAILNAYAPNVFVGY
CPn0892 DEISLLAKDYDYSVDMDTFHKLEQEAKERSRKNVVQSQ---GTSESIYNELHLTSEFIGY
: . : .. . * : *. : :*:: . . . . *: *
sll0362 TDLQSSAIVKAVLV-GGELVDQAVAGQTVQIVLDQTPFYGESGGQIGDKGFLNGDN--LL
L0343 EDKTTQGKLLVSIQ-DDEIVDEVSG--KAQLVFDVTPFYAEMGGQVADHGVIKDAEGQVV
HP1241 ETTECSAKVLGFFDSDFKEITDANPNQEVWVLLEKTPFYAEGGGAIGDRGALFKDNG-EV
CPn0892 DHLSCDTFIEAIIS-KDHIVSSLQEKQEGAIVLKVSPFYAEKGGQVGDSGEIFCSEG-TF
. : : . : . :::. :***.* ** :.* * : : .
sll0362 IRIEDVKRESGIFIHFGRVERGTVQIGTTITATIDRACRRRAQANHTATHLLQSALKRVV
L0343 ANVLDVQHAPHGQNLHSVETLSPLKVGESYTLEIDKERRAAVVKNHTATHLLHAALHNIV
HP1241 AIVLDTKN-FFGLNFSLLEIKKALKKGDQVIAQVSDE-RFEIAKHHSATHLLQSALREVL
CPn0892 IVTHTTSPKAGLIVHHGRISQGSLTVEAAVTAQVNRYRRKRIANNHTACHLLHKALEITL
.. .: :. * :*:* ***: **. :
sll0362 DEGISQAGSLVDFNRLRFDFNSPRAVTMEELQQIEDLINQWIAEAHQTEVAVMPIADAKA
L0343 GNHALQAGSLNEVEFLRFDFTHFAQVTKEELAEIERQVNEVIWQSLKVETVETDIATAKE
HP1241 GSHVSQAGSLVESKRLRFDFSHAKALNDEELEKVEDLVNAQIFKHLNSQVEHMPLNQAKD
CPn0892 GDHIRQAGSYVDDTKIRLDFTHPQAISPEDLLCIETLVNESIRENEPVDIREALYSDVMN
.. **** : :*:**. :. *:* :* :* * : : .
sll0362 KG-AIAMFGEKYGAEVRVIDVPGVSLELCGGTHVANTAEIGLFKIVAETGIAAGVRRIEA
L0343 MG-AMALFGEKYGKNVRVVKIGDYSIELCGGTHTQTTSEIGLFKIVKEEGIGSGVRRIIA
HP1241 KG-ALALFSEKYAENVRVVSFKEASIELCGGIHVENTGLIGGFRIVKESGVSSGVRRIEA
CPn0892 SSEIKQFFGDKYSDVVRVVSAG-HSHELCGGTHAEATGDIGFFRITKEHAVAMGIRRIEA
. :*.:**. ***:. * ***** *. *. ** *:*. * .:. *:*** *
sll0362 VAGPSVLDYLNVREAVVKELGDRLKAKPE-EIPDRVHQLQQELKASQKQLEALKQELALQ
L0343 VTGQKAYEAFKDAENTLNEVATMVKAPQTSQVLAKVTSLQDELKTAQKENDALAGKLAAS
HP1241 VCGKAFYQLAKEENKELKNAKTLLK---NNDVIAGINKLKESVKNSQKAPVSMDLPVEKI
CPn0892 VTGEKAEATVHQQSEVLEEIATLLQVPRD-QIVSRLTATLDERKQQDKRLNELENSLIQT
* * : . ::: :: :: : :. * :* : :
sll0362 KSEQLLTQAQTVGEFKILVADLGTVDGESLKTAAERLQQK-LGESAVVLASIPEEGKVSL
L0343 QSDEIFKNVQTAGSLNFIASEVTVPDANGLRNLADIWKQKELSDVLVLVAKIGE--KVSL
HP1241 HG---------------VNLVVGVVEQGDIKEMIDRLKSKHERLLAMVFKKENE--RITL
CPn0892 KLDKLIHNCHQRQGITCLVHHLAEHENHRLQQYAQCLHQRIPEKLISLWTTEKNGKYIVL
: : : : :: : :.: : . : : *
sll0362 VAAFSPQLVKTKQLKAGQFIGAIAKICGGGGGGRPNLAQAGGRDASKLPEALATAKQTLL
L0343 LVAS-----KSSDVKAGNLVKELAPFVDGRGGGKPDMAMAGGSKAAGIPELLAAVAEKLA
HP1241 ACGV-----KNAPIKANVWANEVAQILGGKGGGRGDFASAGGKDIENLQAALNLAKNTAL
CPn0892 SRVS--DDLITQGVHAQDLLKAVLTPCGGRWGGKDQSAQGSAPALPATEVLNETLWQWIS
. ::* : .* **: : * ... :
sll0362 AELG-
L0343 -----
HP1241 KALEG
CPn0892 TQLI-
-------------------------------------------------------------------------------- Tree construction
CLUSTAL W (1.81) Multiple Sequence Alignments
Sequence format is Clustal
Sequence 1: sll0362 905 aa
Sequence 2: L0343 905 aa
Sequence 3: HP1241 905 aa
Sequence 4: CPn0892 905 aa
Phylogenetic tree file created: [clustal.ph]
+----------------------------------------------------1:sll0362
+--6
| +---------------------------------------------------------2:L0343
--5
| +-----------------------------------------------------------3:HP1241
+--7
+----------------------------------------------------------------4:CPn0892
Midpoint-rooted tree:
+--------------------------------------------------------1:sll0362
+---6
+--7 +-------------------------------------------------------------2:L0343
| |
--5 +----------------------------------------------------------------3:HP1241
|
+-------------------------------------------------------------------4:CPn0892
Remember, this is an unrooted tree!
-------------------------------------------------------------------------------- Bootstrapping tree
CLUSTAL W (1.81) Multiple Sequence Alignments
Sequence format is Clustal
Sequence 1: sll0362 905 aa
Sequence 2: L0343 905 aa
Sequence 3: HP1241 905 aa
Sequence 4: CPn0892 905 aa
Phylogenetic tree file created: [clustal.ph]
No bootstrap generated
This is probably caused by too few input sequences. CLUSTAL needs more than three sequences in order to be able to calculate a phylogenetic tree.
--------------------------------------------------------------------------------
RunClustalW--V1.4--21-Oct-2002/JackL