GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens GW456-L13

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)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963
           Acetyl-coenzyme A synthetase (EC 6.2.1.1)
          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.9023.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: 00:00:00.03
# Mc/sec: 12.04
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 preprint 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