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_4487 PP_4487 acetyl-CoA synthetase

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



>FitnessBrowser__Putida:PP_4487
          Length = 696

 Score = 1243 bits (3216), Expect = 0.0
 Identities = 597/651 (91%), Positives = 623/651 (95%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAA LYPVRPEVAA+TLTDEATYKAMYQQSV+NPDGFWREQA+R+DWIKPFT VKQTSF
Sbjct: 44  MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVS NCLDRHL ERGDQ+AIIWEGDDPSE RNITYRELHE+VCKF
Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G++ PLKANVD ALTNPETSS+QK+IVCKRT G+I W+QHRDIWYEDL
Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVA + CAPKEMGAEEALFILYTSGSTGKPKGV HTT GYL+YAALTHERVFDY+PGEV
Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRV+K++DKHKV+ILYTAPTA
Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMA G AAVEGADGSSLRLLGSVGEPINPEAW+WYYK VGKERCPIVDTWWQTETGG
Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT LKPGSATRPFFGVVPALVDNLGNLI+GAAEGNLVILDSWPGQ+R+LYGD
Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 
Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNAG E SE LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           GLPKTRSGKIMRRILRKIAT EYD LGDISTLADPGVV HLI+THK MN+A
Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLA 694


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: 1751
Number of extensions: 57
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: 696
Length adjustment: 39
Effective length of query: 612
Effective length of database: 657
Effective search space:   402084
Effective search space used:   402084
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 PP_4487 PP_4487 (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.15942.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 1018.9   0.1          0 1018.6   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_4487  PP_4487 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4487  PP_4487 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.6   0.1         0         0       3     628 ..      63     686 ..      61     687 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1018.6 bits;  conditional E-value: 0
                           TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                         +  +yk++y++++ +p+ fw+++a+ +++w+kpf+kv+++s+++   ++kWf+dg+lnvs nc+drh+e+r d++
  lcl|FitnessBrowser__Putida:PP_4487  63 DEATYKAMYQQSVINPDGFWREQAQ-RIDWIKPFTKVKQTSFDDhhvDIKWFADGTLNVSSNCLDRHLEERGDQL 136
                                         5679*********************.5*************99887789*************************** PP

                           TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                         aiiwegd+++e +r++tY+el+++vc++an+l+ + v++gd v+iY+pmipeav+amlacaRiGa+hsvvf+Gfs
  lcl|FitnessBrowser__Putida:PP_4487 137 AIIWEGDDPSE-HRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFS 210
                                         *********96.*************************************************************** PP

                           TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelv 223
                                         +eala Ri+d+++k+vitadeg+Rgg++++lk++vd al++ e+ sv+k++v+krtg ++a w++ rD+w+e+l+
  lcl|FitnessBrowser__Putida:PP_4487 211 PEALAGRIIDCKSKVVITADEGVRGGRRTPLKANVDLALTNPETsSVQKIIVCKRTGGDIA-WHQHRDIWYEDLM 284
                                         *****************************************9998**************77.************* PP

                           TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                         +  as++c+p+++++e+ lfiLYtsGstGkPkGvlhttgGyl++aalt++ vfd+++++++wCtaDvGWvtGhsY
  lcl|FitnessBrowser__Putida:PP_4487 285 KV-ASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEVYWCTADVGWVTGHSY 358
                                         *5.************************************************************************ PP

                           TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373
                                         ivygPLanGattllfegvp+ypd  r+ ++++k+kv+i+YtaPtaiRa+m++g+++v+  d sslr+lgsvGepi
  lcl|FitnessBrowser__Putida:PP_4487 359 IVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTAIRAMMAEGQAAVEGADGSSLRLLGSVGEPI 433
                                         *************************************************************************** PP

                           TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                         npeaw+Wyy++vGke+cpivdtwWqtetGgili+plpg at lkpgsat+P+fG+ +++vd+ g+ ++  +e g 
  lcl|FitnessBrowser__Putida:PP_4487 434 NPEAWNWYYKTVGKERCPIVDTWWQTETGGILISPLPG-ATGLKPGSATRPFFGVVPALVDNLGNLIDGAAE-GN 506
                                         **************************************.6****************************8777.79 PP

                           TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523
                                         Lvi ++wP++ r++ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+
  lcl|FitnessBrowser__Putida:PP_4487 507 LVILDSWPGQSRSLYGDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVA 581
                                         *************************************************************************** PP

                           TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598
                                         h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimR
  lcl|FitnessBrowser__Putida:PP_4487 582 HSKVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASE-QLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 655
                                         ********************************999.6************************************** PP

                           TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628
                                         R+lrkia+ge ++lgd+stl+dp vv++l++
  lcl|FitnessBrowser__Putida:PP_4487 656 RILRKIATGEyDALGDISTLADPGVVQHLID 686
                                         ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (696 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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 10.17
//
[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