Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo3_N2E3:AO353_03060
(651 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963
Length = 651
Score = 1295 bits (3352), Expect = 0.0
Identities = 623/651 (95%), Positives = 639/651 (98%)
Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
MSAASLYPVRPEV ANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1 MSAASLYPVRPEVLANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDPAESRNITYRELHEQVCKF
Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEQVCKF 120
Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDC+S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRS 180
Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRTGG+IKWNQHRDIW+EDL
Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTGGDIKWNQHRDIWFEDL 240
Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAA+THERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHERVFDYRPGEI 300
Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
YWCTADVGWVTGH+YIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360
Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
IRAMMA GTAAVEGADGSSLRLLGSVGEPINPEAW+WYYKNVG+SRCPIVDTWWQTETG
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKSRCPIVDTWWQTETGG 420
Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
+MSPLPGAH LKPGSAARPFFGVVPALVDNLGNI+EG AEGNLVILDSWPGQARTL+GD
Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNIVEGEAEGNLVILDSWPGQARTLFGD 480
Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
HDRFVDTYFKTFRGMYFTGDGARRDADGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
KVAEAAVVGVPHDIKGQGIYVYVTL GEEP+E LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEQLRLELKNWVRKEIGPIASPDVIQWAP 600
Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
GLPKTRSGKIMRRILRKIAT EY+GLGDISTLADP VVQHLIDTHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYEGLGDISTLADPSVVQHLIDTHKTMNVA 651
Lambda K H
0.319 0.136 0.425
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1747
Number of extensions: 55
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space: 375769
Effective search space used: 375769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate PfGW456L13_1963 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR02188.hmm
# target sequence database: /tmp/gapView.3205.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02188 [M=629]
Accession: TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1023.9 0.1 0 1023.7 0.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1023.7 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98
Alignments for each domain:
== domain 1 score: 1023.7 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedg 54
+ +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADG 73
5679*********************5.*************99887789******* PP
TIGR02188 55 elnvsyncvdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkel 109
+lnvsync+drh+++r d+vaiiwegd++ e sr++tY+el+++vc++an+l+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 74 TLNVSYNCLDRHLAERGDQVAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQ 127
*****************************96.*********************** PP
TIGR02188 110 GvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdaeakl 164
v++gd v+iY+pmipeav+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 128 DVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRSKV 182
******************************************************* PP
TIGR02188 165 vitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
vitadeg+R gk+i+lk++vd+al++ e+ s++kv+v+krtg +++ w++ rD+w
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 183 VITADEGIRAGKKIPLKANVDDALTNPETsSIQKVIVCKRTGGDIK-WNQHRDIW 236
**************************9998**************76.******** PP
TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvk 273
+e+l++ a + c+p+++++e+ lfiLYtsGstGkPkGv+httgGyll+aa+t++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 237 FEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHE 290
******5.*********************************************** PP
TIGR02188 274 yvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwev 328
vfd+++++i+wCtaDvGWvtGhsYivygPLanGattllfegvp+ypd r++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 291 RVFDYRPGEIYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKI 345
******************************************************* PP
TIGR02188 329 iekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyye 383
++k+kv+i+YtaPtaiRa+m+ g+++v+ d sslr+lgsvGepinpeaw+Wyy+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 346 VDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYK 400
******************************************************* PP
TIGR02188 384 vvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
+vGk++cpivdtwWqtetGg +++plpg a +lkpgsa++P+fG+ +++vd+ g+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 401 NVGKSRCPIVDTWWQTETGGNMMSPLPG-AHALKPGSAARPFFGVVPALVDNLGN 454
****************************.6************************* PP
TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdG 493
ve e+e g Lvi ++wP+++rt++gd++rfv+tYfk+++g+yftGDgarrd+dG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 455 IVEGEAE-GNLVILDSWPGQARTLFGDHDRFVDTYFKTFRGMYFTGDGARRDADG 508
***8888.79********************************************* PP
TIGR02188 494 yiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafv 548
y+wi+GRvDdv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 509 YYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYV 563
******************************************************* PP
TIGR02188 549 vlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrk 603
+lk+g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimRR+lrk
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 564 TLKNGEEPNE-QLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRK 617
*********9.6******************************************* PP
TIGR02188 604 iaege.ellgdvstledpsvveelke 628
ia+ e e lgd+stl+dpsvv++l++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 618 IATAEyEGLGDISTLADPSVVQHLID 643
*****9****************9975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (651 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.17
# Mc/sec: 2.35
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory