Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659
          Length = 646

 Score = 1313 bits (3399), Expect = 0.0
 Identities = 637/646 (98%), Positives = 644/646 (99%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           +YPVRPEVAA+TLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV
Sbjct: 1   VYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 60

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
           DIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDP+ESRNITYRELHEEVCKFANALR
Sbjct: 61  DIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEEVCKFANALR 120

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
           GQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT
Sbjct: 121 GQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 180

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG
Sbjct: 181 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 240

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
           TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPG+VYWCTA
Sbjct: 241 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTA 300

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKV+DKHKV+ILYTAPTAIRAMM
Sbjct: 301 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVVDKHKVNILYTAPTAIRAMM 360

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
           ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP
Sbjct: 361 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 420

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV
Sbjct: 421 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 480

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
           DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA
Sbjct: 481 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 540

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT
Sbjct: 541 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 600

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           RSGKIMRRILRKIATAEYDGLGDISTLADP VVAHLIETHKTMNVA
Sbjct: 601 RSGKIMRRILRKIATAEYDGLGDISTLADPSVVAHLIETHKTMNVA 646


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: 1717
Number of extensions: 46
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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 Pf6N2E2_5659 (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.8010.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 1025.9   0.2          0 1025.7   0.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  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 ! 1025.7   0.2         0         0       3     628 ..      15     638 ..      13     639 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1025.7 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__pseudo6_N2E2:Pf6N2E2_5659  15 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCL 77 
                                                    5679*********************5.*************99887789**************** PP

                                      TIGR02188  64 drhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127
                                                    drh+++r d+vaiiwegd++ e sr++tY+el++evc++an+l+ + v++gd v+iY+pmipea
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  78 DRHLAERGDQVAIIWEGDDPAE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEA 140
                                                    ********************96.***************************************** PP

                                      TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191
                                                    v+amlacaRiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 141 VVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDALTNP 204
                                                    ***************************************************************9 PP

                                      TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkP 254
                                                    e+ s++kv+v+krt  +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGstGkP
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 205 ETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKP 266
                                                    998**************76.**************5.**************************** PP

                                      TIGR02188 255 kGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvpt 318
                                                    kGv+htt+Gyll+aalt++ vfd+k++d++wCtaDvGWvtGhsYivygPLanGattllfegvp+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 267 KGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPN 330
                                                    **************************************************************** PP

                                      TIGR02188 319 ypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyy 382
                                                    ypd  r+++v++k+kv+i+YtaPtaiRa+m+ g+++v+  d sslr+lgsvGepinpeaw+Wyy
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 331 YPDITRVAKVVDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYY 394
                                                    **************************************************************** PP

                                      TIGR02188 383 evvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446
                                                    ++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ +e  +e 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 395 KNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNLIEGAAE- 456
                                                    *****************************.6****************************8777. PP

                                      TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                                    g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGh
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 457 GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGH 520
                                                    79************************************************************** PP

                                      TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeig 574
                                                    r+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeig
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 521 RMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLELKNWVRKEIG 583
                                                    *********************************************999.6************** PP

                                      TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                    pia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dpsvv++l+e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 584 PIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPSVVAHLIE 638
                                                    **********************************9****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.89
//
[ok]

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

Downloads

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

Related tools

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