Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_03060 AO353_03060 acetyl-CoA synthetase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03060
          Length = 651

 Score = 1340 bits (3469), Expect = 0.0
 Identities = 651/651 (100%), Positives = 651/651 (100%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL
Sbjct: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA
Sbjct: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
           TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD
Sbjct: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480

Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
           GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 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: 1791
Number of extensions: 63
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 AO353_03060 AO353_03060 (acetyl-CoA synthetase)
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.609401.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 1013.5   0.1          0 1013.3   0.1    1.0  1  FitnessBrowser__pseudo3_N2E3:AO353_03060  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo3_N2E3:AO353_03060  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1013.3   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1013.3 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhve 68 
                                               +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync+drh++
  FitnessBrowser__pseudo3_N2E3:AO353_03060  20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCLDRHLA 87 
                                               5679*********************5.*************99887789********************* PP

                                 TIGR02188  69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRi 137
                                               +r d++aiiwegd++ e sr++tY+el+++vc++an+l+ + v++gd v+iY+pmipeav+amlac+Ri
  FitnessBrowser__pseudo3_N2E3:AO353_03060  88 ERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRI 155
                                               ***************96.*************************************************** PP

                                 TIGR02188 138 GavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtg 205
                                               Ga+hsvvf+Gfs+eala Ri+d+++k+vitadeglR gk+i+lk++vd+al++ e+ s++kv+v+krtg
  FitnessBrowser__pseudo3_N2E3:AO353_03060 156 GAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGLRAGKKISLKANVDDALTNPETsSIQKVIVCKRTG 224
                                               *****************************************************9998************ PP

                                 TIGR02188 206 eevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvky 274
                                                +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGstGkPkGv+httgGyll+aalt++ 
  FitnessBrowser__pseudo3_N2E3:AO353_03060 225 GNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHER 291
                                               **76.**************5.************************************************ PP

                                 TIGR02188 275 vfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPta 343
                                               vfd+++++i+wCtaDvGWvtGh+YivygPLanGattllfegvp+ypd  r++++i+k+kv+i+YtaPta
  FitnessBrowser__pseudo3_N2E3:AO353_03060 292 VFDYRPGEIYWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
                                               ********************************************************************* PP

                                 TIGR02188 344 iRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgv 412
                                               iRa+m++g+++v+  d sslr+lgsvGepinpeaweWyy++vG+++cpivdtwWqtetG++l++plpg 
  FitnessBrowser__pseudo3_N2E3:AO353_03060 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPLPG- 428
                                               ********************************************************************. PP

                                 TIGR02188 413 atelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkgly 481
                                               a  lkpgsa++P+fG+ +++vd+ g+ +e  +e g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+y
  FitnessBrowser__pseudo3_N2E3:AO353_03060 429 AHGLKPGSAARPFFGVVPALVDNLGNIIEGVAE-GNLVILDSWPGQARTLYGDHDRFVDTYFKTFRGMY 496
                                               6***************************98777.79********************************* PP

                                 TIGR02188 482 ftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvl 550
                                               ftGDgarrd+dGy wi+GRvDdv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l
  FitnessBrowser__pseudo3_N2E3:AO353_03060 497 FTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTL 565
                                               ********************************************************************* PP

                                 TIGR02188 551 kegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstle 618
                                               + g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ge + lgd+stl+
  FitnessBrowser__pseudo3_N2E3:AO353_03060 566 NGGEEPSE-ALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATGEyDGLGDISTLA 633
                                               *******9.5************************************************9********** PP

                                 TIGR02188 619 dpsvveelke 628
                                               dp vv++l++
  FitnessBrowser__pseudo3_N2E3:AO353_03060 634 DPGVVQHLID 643
                                               ******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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 40.57
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources