Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2C3

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO356_18695 AO356_18695 acetyl-CoA synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18695
          Length = 651

 Score = 1332 bits (3448), Expect = 0.0
 Identities = 651/651 (100%), Positives = 651/651 (100%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL
Sbjct: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD
Sbjct: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651


Lambda     K      H
   0.318    0.135    0.418 

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: 1737
Number of extensions: 47
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate AO356_18695 AO356_18695 (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.15117.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 1021.5   0.2          0 1021.2   0.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  AO356_18695 acetyl-CoA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  AO356_18695 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.2   0.2         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1021.2 bits;  conditional E-value: 0
                                       TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsync 62 
                                                     +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNC 81 
                                                     5679*********************5.*************99887789*************** PP

                                       TIGR02188  63 vdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmip 125
                                                     +drh+++r d++aiiwegd+++e sr++tY+el++evc++an+l+ + v++gd v+iY+pmip
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  82 LDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIP 143
                                                     *********************96.*************************************** PP

                                       TIGR02188 126 eaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdeal 188
                                                     eav+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 144 EAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDAL 206
                                                     *************************************************************** PP

                                       TIGR02188 189 ekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGs 250
                                                     ++ e+ s++kv+v+krt  +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGs
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 207 TNPETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGS 267
                                                     **9998**************76.**************5.************************ PP

                                       TIGR02188 251 tGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllf 313
                                                     tGkPkGv+htt+Gyll+aalt++ vfd+k+++++wCtaDvGWvtGhsYivygPLanGattllf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 268 TGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLF 330
                                                     *************************************************************** PP

                                       TIGR02188 314 egvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376
                                                     egvp+ypd  r+++vi+k+kv+i+YtaPtaiRa+m+ g+++v+  d sslr+lgsvGepinpe
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 331 EGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPE 393
                                                     *************************************************************** PP

                                       TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                                     aw+Wyy++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 394 AWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNL 455
                                                     ***********************************.6************************** PP

                                       TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvD 502
                                                     +e  +e g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvD
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 456 IEGAAE-GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVD 517
                                                     **8777.79****************************************************** PP

                                       TIGR02188 503 dvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekel 565
                                                     dv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ el
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 518 DVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLEL 579
                                                     *****************************************************999.6***** PP

                                       TIGR02188 566 kklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                                     k++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dp vv++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 580 KNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPGVVAHLI 642
                                                     *******************************************9****************998 PP

                                       TIGR02188 628 e 628
                                                     e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 643 E 643
                                                     6 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.90
//
[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 (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 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