Alignments for a candidate for acs in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas putida KT2440

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4702 PP_4702 acetyl-CoA synthetase

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



>FitnessBrowser__Putida:PP_4702
          Length = 644

 Score =  861 bits (2224), Expect = 0.0
 Identities = 408/637 (64%), Positives = 491/637 (77%), Gaps = 4/637 (0%)

Query: 7   YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YP    V+ +       Y+ +Y+QSV +PD FW EQAKRLDWIKP+++V+Q   D H   
Sbjct: 7   YPQALAVSQSAALTPEDYRRLYRQSVEDPDTFWAEQAKRLDWIKPWSSVQQC--DLHTGK 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKFANALRG 126
            +WF    LNVSYNC+DRHLA+RG+Q A++WEGDDP +S+ ITYRELH QVC+ ANA++ 
Sbjct: 65  ARWFDGAQLNVSYNCIDRHLAQRGEQTALLWEGDDPKDSKAITYRELHRQVCRLANAMKA 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           + V +GD V+IYMPMIPEA  AMLACTRIGAIHSVVFGGFSP+AL  RI+D   + VITA
Sbjct: 125 RGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDALRDRILDADCRTVITA 184

Query: 187 DEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGT 246
           DEG+R GK+I LK NVD AL +    ++  V+V +RTGG++ W + RD+WY +  K AG 
Sbjct: 185 DEGVRGGKRIPLKQNVDKALAS--CPAVSSVLVVRRTGGDVAWTEGRDLWYHEATKDAGD 242

Query: 247 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTAD 306
            C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL A +T + VFDYR GE++WCTAD
Sbjct: 243 DCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTAD 302

Query: 307 VGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMA 366
           VGWVTGH+YIVYGPLANGA +L+FEGVPNYPD +R  +++DKH+VNI YTAPTA+RA+M 
Sbjct: 303 VGWVTGHSYIVYGPLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMR 362

Query: 367 QGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPL 426
           +G+A ++     SLRLLGSVGEPINPEAWEWY++ VGQ RCPIVDTWWQTETG  +++PL
Sbjct: 363 EGSAPLQSTSRKSLRLLGSVGEPINPEAWEWYFEEVGQKRCPIVDTWWQTETGGIMLTPL 422

Query: 427 PGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVD 486
           PG   LKPG A +P FGV P L+D  G +IEG   G L I  SWPGQ R++YGDH R VD
Sbjct: 423 PGTQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGAGVLAIKASWPGQIRSVYGDHQRMVD 482

Query: 487 TYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 546
           TYFK   G YFTGDGARRDADG +WITGR+DDV+NVSGHR+GTAE+ESA+V H  VAEAA
Sbjct: 483 TYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSVAEAA 542

Query: 547 VVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 606
           VVG PHD+KGQG+Y +VT   G  P + L+ EL   V KEIG  A P++IQWAP LPKTR
Sbjct: 543 VVGYPHDLKGQGVYAFVTTMNGVTPDDTLKAELLALVSKEIGSFAKPELIQWAPALPKTR 602

Query: 607 SGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643
           SGKIMRRILRKIA  E + LGD STLADP VVQ LID
Sbjct: 603 SGKIMRRILRKIACNELENLGDTSTLADPSVVQGLID 639


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: 1451
Number of extensions: 70
Number of successful extensions: 3
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: 644
Length adjustment: 38
Effective length of query: 613
Effective length of database: 606
Effective search space:   371478
Effective search space used:   371478
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 PP_4702 PP_4702 (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.15311.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 1039.4   0.0          0 1039.2   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4702  PP_4702 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4702  PP_4702 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1039.2   0.0         0         0       4     628 ..      21     639 ..      18     640 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1039.2 bits;  conditional E-value: 0
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                          e+y++ly++++edp++fwa++ak+ l+w+kp+++v++++l++ k++Wf++++lnvsync+drh+++r +++a+ 
  lcl|FitnessBrowser__Putida:PP_4702  21 PEDYRRLYRQSVEDPDTFWAEQAKR-LDWIKPWSSVQQCDLHTgKARWFDGAQLNVSYNCIDRHLAQRGEQTALL 94 
                                         689*********************5.***************999******************************* PP

                           TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                         wegd+++ ds+++tY+el+r+vcrlan++k+ Gvkkgdrv+iY+pmipea++amlac+RiGa+hsvvf+Gfs++a
  lcl|FitnessBrowser__Putida:PP_4702  95 WEGDDPK-DSKAITYRELHRQVCRLANAMKARGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDA 168
                                         ******9.5****************************************************************** PP

                           TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekea 227
                                         l++Ri da++++vitadeg+Rggk+i+lk++vd+al++++ +v++vlvv+rtg +va w+egrD+w++e++++ a
  lcl|FitnessBrowser__Putida:PP_4702 169 LRDRILDADCRTVITADEGVRGGKRIPLKQNVDKALASCP-AVSSVLVVRRTGGDVA-WTEGRDLWYHEATKD-A 240
                                         ***************************************9.7*************77.**************7.* PP

                           TIGR02188 228 saecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                          ++c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+a++t+k+vfd++d+++fwCtaDvGWvtGhsYivyg
  lcl|FitnessBrowser__Putida:PP_4702 241 GDDCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTADVGWVTGHSYIVYG 315
                                         *************************************************************************** PP

                           TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpea 377
                                         PLanGa +l+fegvp+ypd+srfw+v++k++v+ifYtaPta+Ralm++g++ +++++++slr+lgsvGepinpea
  lcl|FitnessBrowser__Putida:PP_4702 316 PLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMREGSAPLQSTSRKSLRLLGSVGEPINPEA 390
                                         *************************************************************************** PP

                           TIGR02188 378 weWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvik 452
                                         weWy+e+vG+++cpivdtwWqtetGgi++tplpg + +lkpg+at+P+fG++++++de+gk +e     gvL+ik
  lcl|FitnessBrowser__Putida:PP_4702 391 WEWYFEEVGQKRCPIVDTWWQTETGGIMLTPLPG-TQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGA-GVLAIK 463
                                         **********************************.6***************************97666.8***** PP

                           TIGR02188 453 kpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheav 527
                                          +wP+++r++ygd++r+v+tYfk l+g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h++v
  lcl|FitnessBrowser__Putida:PP_4702 464 ASWPGQIRSVYGDHQRMVDTYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSV 538
                                         *************************************************************************** PP

                           TIGR02188 528 aeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllr 602
                                         aeaavvg+p+++kg+ ++afv+ ++gv++d++ l++el +lv+keig++akp+ i+++++lPktRsGkimRR+lr
  lcl|FitnessBrowser__Putida:PP_4702 539 AEAAVVGYPHDLKGQGVYAFVTTMNGVTPDDT-LKAELLALVSKEIGSFAKPELIQWAPALPKTRSGKIMRRILR 612
                                         *******************************5.****************************************** PP

                           TIGR02188 603 kiaege.ellgdvstledpsvveelke 628
                                         kia +e e+lgd+stl+dpsvv+ l++
  lcl|FitnessBrowser__Putida:PP_4702 613 KIACNElENLGDTSTLADPSVVQGLID 639
                                         **********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (644 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.83
//
[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
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