Alignments for a candidate for acs in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas stutzeri RCH2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF2607 Psest_2657 acetate--CoA ligase

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



>FitnessBrowser__psRCH2:GFF2607
          Length = 651

 Score = 1132 bits (2927), Expect = 0.0
 Identities = 534/648 (82%), Positives = 588/648 (90%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           M AAS+YPV PE A  +LTDEA Y+AMYQQSV+NP+GFWREQA RL+WI+PFT VK+TSF
Sbjct: 1   MCAASVYPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVS NCLDRHLAERGDQ+AIIWEGD+PSE R ITYREL++EVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEA VAMLAC RIGAIHSVVFGGFSPEALAGRIID +S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEG+R GK IPLK NVD+ALT+P+T  +QK+IV +RT  +I+W+ HRD+ Y+DL
Sbjct: 181 KVVITADEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M+VAG VCAPKEMGAEE LFILYTSGSTGKPKGV HT  GYLLYAALTHERVFDY+PG+V
Sbjct: 241 MRVAGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTAD+GW+TGHSY++YGPLANGATTL++EGVPNYPD+TR+A++IDKH+V+ILYTAPTA
Sbjct: 301 YWCTADIGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMA G AA+EGADGSSLRLLG+VGEPINPEAW WYY+ VG+ RCPIVDTWWQTETGG
Sbjct: 361 IRAMMAEGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGATALKPGSATRP FGVVP LVDNLGNL+EG AEGNLVILDSWPGQ RT+Y D
Sbjct: 421 ILISPLPGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHA 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAA VGVPH +KGQ IYVYVTL AG E S+ LR EL+ WVR EIGPIA PD IQWAP
Sbjct: 541 KVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTM 648
           GLPKTRSGKIMRR+LRKIAT +YD LGD STLADPGVV  LIE H+ +
Sbjct: 601 GLPKTRSGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAV 648


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: 1625
Number of extensions: 60
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 GFF2607 Psest_2657 (acetate--CoA ligase)
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.29509.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.1e-307 1005.5   0.0   4.8e-307 1005.3   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2607  Psest_2657 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2607  Psest_2657 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1005.3   0.0  4.8e-307  4.8e-307       4     628 ..      21     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1005.3 bits;  conditional E-value: 4.8e-307
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           +y+++y++++ +pe fw+++a  +l+w++pf++v+++s+++   ++kWf+dg+lnvs+nc+drh+++r d+va
  lcl|FitnessBrowser__psRCH2:GFF2607  21 EAAYRAMYQQSVINPEGFWREQAA-RLNWIRPFTEVKRTSFDDhhvDIKWFADGTLNVSANCLDRHLAERGDQVA 94 
                                         678*********************.5*************99887789**************************** PP

                           TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                         iiwegde++e +r++tY+el++evc++an+l+ + v++gd v+iY+pmipea++amlacaRiGa+hsvvf+Gfs+
  lcl|FitnessBrowser__psRCH2:GFF2607  95 IIWEGDEPSE-HREITYRELYQEVCKFANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSP 168
                                         ********96.**************************************************************** PP

                           TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelve 224
                                         eala Ri+d ++k+vitadeg+Rggk i+lk++vdeal++ ++  v+k++vv+rtg+++  w+  rDv +++l++
  lcl|FitnessBrowser__psRCH2:GFF2607 169 EALAGRIIDGQSKVVITADEGIRGGKPIPLKENVDEALTHPQTrCVQKIIVVRRTGADIR-WHPHRDVCYDDLMR 242
                                         ****************************************99889*************76.************** PP

                           TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYi 299
                                           a + c+p+++++e+plfiLYtsGstGkPkGvlht gGyll+aalt++ vfd++++d++wCtaD+GW+tGhsY+
  lcl|FitnessBrowser__psRCH2:GFF2607 243 V-AGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDVYWCTADIGWITGHSYL 316
                                         5.************************************************************************* PP

                           TIGR02188 300 vygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepin 374
                                         +ygPLanGattl++egvp+ypd  r++++i+k++v+i+YtaPtaiRa+m++g ++++  d sslr+lg+vGepin
  lcl|FitnessBrowser__psRCH2:GFF2607 317 IYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTAIRAMMAEGAAAMEGADGSSLRLLGTVGEPIN 391
                                         *************************************************************************** PP

                           TIGR02188 375 peaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449
                                         peaw+Wyye+vG+++cpivdtwWqtetGgili+plpg at+lkpgsat+PlfG+ + +vd+ g+ +e  +e g L
  lcl|FitnessBrowser__psRCH2:GFF2607 392 PEAWHWYYETVGRSRCPIVDTWWQTETGGILISPLPG-ATALKPGSATRPLFGVVPGLVDNLGNLLEGPAE-GNL 464
                                         *************************************.6****************************7666.68* PP

                           TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsh 524
                                         vi ++wP+++rtiy+d++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+h
  lcl|FitnessBrowser__psRCH2:GFF2607 465 VILDSWPGQMRTIYRDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
                                         *************************************************************************** PP

                           TIGR02188 525 eavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRR 599
                                          +vaeaa+vgvp+ +kg+ai+++v+l +gve++++ l++el+++vr+eigpia pd+i++++ lPktRsGkimRR
  lcl|FitnessBrowser__psRCH2:GFF2607 540 AKVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDT-LRQELQQWVRHEIGPIAVPDTIQWAPGLPKTRSGKIMRR 613
                                         **********************************5.*************************************** PP

                           TIGR02188 600 llrkiaege.ellgdvstledpsvveelke 628
                                         llrkia+++ ++lgd+stl+dp vv++l+e
  lcl|FitnessBrowser__psRCH2:GFF2607 614 LLRKIATDDyDALGDTSTLADPGVVDQLIE 643
                                         *********9*****************987 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.35
//
[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