Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N1B4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf1N1B4_3430 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430
          Length = 651

 Score = 1304 bits (3375), Expect = 0.0
 Identities = 629/651 (96%), Positives = 641/651 (98%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEV ANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVLANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDC+S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRS 180

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRTGG+IKWNQHRDIW+EDL
Sbjct: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTGGDIKWNQHRDIWFEDL 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+WYYKNVGQSRCPIVDTWWQTETG 
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGQSRCPIVDTWWQTETGG 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
           KVAEAAVVGVPHDIKGQGIYVYVTLN GEEPSE LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEEPSEQLRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
           GLPKTRSGKIMRRILRKIAT EYDGLGDISTLADPGVVQHLIDTHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVQHLIDTHKTMNVA 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: 1757
Number of extensions: 59
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 Pf1N1B4_3430 (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.25341.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 1020.1   0.1          0 1019.9   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430  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 ! 1019.9   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1019.9 bits;  conditional E-value: 0
                                      TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncv 63 
                                                    +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430  20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCL 82 
                                                    5679*********************5.*************99887789**************** PP

                                      TIGR02188  64 drhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127
                                                    drh+++r d++aiiwegd++ e sr++tY+el+++vc++an+l+ + v++gd v+iY+pmipea
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430  83 DRHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEA 145
                                                    ********************96.***************************************** PP

                                      TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191
                                                    v+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 146 VVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRSKVVITADEGVRAGKKIPLKANVDDALTNP 209
                                                    ***************************************************************9 PP

                                      TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkP 254
                                                    e+ s++kv+v+krtg +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGstGkP
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 210 ETsSIQKVIVCKRTGGDIK-WNQHRDIWFEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKP 271
                                                    998**************76.**************5.**************************** PP

                                      TIGR02188 255 kGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvpt 318
                                                    kGv+httgGyll+aa+t++ vfd+++++i+wCtaDvGWvtGhsYivygPLanGattllfegvp+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 272 KGVQHTTGGYLLYAAMTHERVFDYRPGEIYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPN 335
                                                    **************************************************************** PP

                                      TIGR02188 319 ypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyy 382
                                                    ypd  r++++++k+kv+i+YtaPtaiRa+m+ g+++v+  d sslr+lgsvGepinpeaw+Wyy
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 336 YPDITRVAKIVDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYY 399
                                                    **************************************************************** PP

                                      TIGR02188 383 evvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446
                                                    ++vG+++cpivdtwWqtetGg +++plpg a +lkpgsa++P+fG+ +++vd+ g+ ve e+e 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 400 KNVGQSRCPIVDTWWQTETGGNMMSPLPG-AHALKPGSAARPFFGVVPALVDNLGNIVEGEAE- 461
                                                    *****************************.6****************************8888. PP

                                      TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                                    g Lvi ++wP+++rt++gd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGh
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 462 GNLVILDSWPGQARTLFGDHDRFVDTYFKTFRGMYFTGDGARRDADGYYWITGRVDDVLNVSGH 525
                                                    79************************************************************** PP

                                      TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeig 574
                                                    r+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeig
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 526 RMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEEPSE-QLRLELKNWVRKEIG 588
                                                    ***********************************************9.6************** PP

                                      TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                    pia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dp vv++l++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3430 589 PIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPGVVQHLID 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.63
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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

GapMind for catabolism of small carbon sources