Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BPHYT_RS07000 BPHYT_RS07000 acetyl-CoA synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__BFirm:BPHYT_RS07000
          Length = 660

 Score = 1120 bits (2898), Expect = 0.0
 Identities = 526/659 (79%), Positives = 595/659 (90%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MSAIESV+ E RVF P    A+ AAI  M+AY+AL  EAE DYEGFW R ARE L W  P
Sbjct: 1   MSAIESVLHERRVFPPSAEAAAGAAISGMDAYRALAAEAESDYEGFWGRLARETLSWNTP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLD++NAPFY WFEDG++NASYN +DR+++ GN ++VAI+FEADDG+VT VTY++L 
Sbjct: 61  FTKVLDETNAPFYTWFEDGQINASYNSIDRHVEAGNGERVAIIFEADDGTVTNVTYQDLL 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +V RFAN LK  G++KGDRVVIYMPMS+EG+VAMQACAR+GATHSVVFGGFS+KSL ER
Sbjct: 121 QRVSRFANALKKRGVKKGDRVVIYMPMSIEGIVAMQACARIGATHSVVFGGFSSKSLNER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           LVDVGAVAL+T+DEQMRGGKALPLK IAD+ALA+GGCEAV +VIVY+RTGGKVAW EGRD
Sbjct: 181 LVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCEAVTSVIVYQRTGGKVAWNEGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            WM +++  + D C  E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA  T+KWTFD
Sbjct: 241 LWMHELTQAESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTLKWTFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
            KP D+FWCTADIGW+TGH+YI YGPL  G TQVVFEGVPTYPNAGRFWDMIA+HKVS+F
Sbjct: 301 WKPSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVSLF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKAA+AD+K+HPK YDLS+LR++GTVGEPINPEAW+WYY+N+G  RCPIV
Sbjct: 361 YTAPTAIRSLIKAADADQKVHPKSYDLSTLRIIGTVGEPINPEAWIWYYENVGGSRCPIV 420

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAA+VDETG DVPNG GGILVVKRPW
Sbjct: 421 DTWWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAVVDETGQDVPNGQGGILVVKRPW 480

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+M+R +WGDP+R++KSYFPEELGGKLYLAGDG++RDKDTGYFTIMGRIDDVLNVSGHR+
Sbjct: 481 PSMLRNVWGDPDRYKKSYFPEELGGKLYLAGDGAVRDKDTGYFTIMGRIDDVLNVSGHRL 540

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALVSNPLVAEAAVVGRPD  TGEA+CAFVVLKR+RP GEEAVK+A ELRNWVG
Sbjct: 541 GTMEIESALVSNPLVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEAVKLANELRNWVG 600

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           KEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRSLAKGEEITQD STLENPAIL+QL ++
Sbjct: 601 KEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENPAILDQLGES 659


Lambda     K      H
   0.319    0.136    0.422 

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: 1590
Number of extensions: 70
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: 660
Length of database: 660
Length adjustment: 38
Effective length of query: 622
Effective length of database: 622
Effective search space:   386884
Effective search space used:   386884
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 BPHYT_RS07000 BPHYT_RS07000 (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.20064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     3e-296  969.7   0.0   3.4e-296  969.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07000  BPHYT_RS07000 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07000  BPHYT_RS07000 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  969.5   0.0  3.4e-296  3.4e-296       2     627 ..      27     657 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 969.5 bits;  conditional E-value: 3.4e-296
                                TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                              + +++y++l +ea++d+e fw++la+e+l+w +pf+kvlde+++p+++Wfedg++n+syn++drhve+ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000  27 SGMDAYRALAAEAESDYEGFWGRLARETLSWNTPFTKVLDETNAPFYTWFEDGQINASYNSIDRHVEAgN 96 
                                              5789****************************************************************** PP

                                TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140
                                               ++vaii+e+d+ +  + ++tY++ll++v+r+an+lk+ Gvkkgdrv+iY+pm +e ++am+acaRiGa+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000  97 GERVAIIFEADDGT--VTNVTYQDLLQRVSRFANALKKRGVKKGDRVVIYMPMSIEGIVAMQACARIGAT 164
                                              ***********664..8***************************************************** PP

                                TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeeva 209
                                              hsvvf+Gfs+++l+eR+vd+ a  ++t+de++Rggk+++lk+i+deal++  + +v +v+v++rtg +va
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 165 HSVVFGGFSSKSLNERLVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCeAVTSVIVYQRTGGKVA 234
                                              **************************************************99889*************77 PP

                                TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279
                                               w+egrD+w++el++  +s++c+pe++++e+plfiLYtsGstGkPkGv+h+tgGyll+aa t k++fd k
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 235 -WNEGRDLWMHELTQA-ESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTLKWTFDWK 302
                                              .**************5.***************************************************** PP

                                TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmk 349
                                              ++d+fwCtaD+GW+tGhsYi ygPL+ G t+++fegvptyp+a+rfw++i k+kv+ fYtaPtaiR+l+k
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 303 PSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVSLFYTAPTAIRSLIK 372
                                              ********************************************************************** PP

                                TIGR02188 350 lgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                              ++++    ++k++dls+lr++g+vGepinpeaw Wyye+vG ++cpivdtwWqtetGg++itplpg at+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 373 AADAdqkvHPKSYDLSTLRIIGTVGEPINPEAWIWYYENVGGSRCPIVDTWWQTETGGHMITPLPG-ATP 441
                                              985422337899******************************************************.6** PP

                                TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyft 483
                                              l pgs+tlPl+Gi+a+vvde+g++v ++++ g+Lv+k+pwPsmlr ++gd++r+ ++Yf +  g  ly++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 442 LVPGSCTLPLPGIMAAVVDETGQDVPNGQG-GILVVKRPWPSMLRNVWGDPDRYKKSYFPEELGgkLYLA 510
                                              ***************************999.8***************************9876567**** PP

                                TIGR02188 484 GDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552
                                              GDga+rdkd Gy++i+GR+Ddv+nvsGhrlgt+eiesalvs++ vaeaavvg+pd ++gea++afvvlk+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 511 GDGAVRDKDtGYFTIMGRIDDVLNVSGHRLGTMEIESALVSNPLVAEAAVVGRPDATTGEAVCAFVVLKR 580
                                              ********99************************************************************ PP

                                TIGR02188 553 gveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620
                                              ++ e ee  +l++el+++v keigpiakp++i++ e+lPktRsGkimRRllr++a+gee+++dvstle+p
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 581 ARPEGEEavKLANELRNWVGKEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENP 650
                                              99988887799*********************************************************** PP

                                TIGR02188 621 svveelk 627
                                              +++++l 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07000 651 AILDQLG 657
                                              ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (660 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: 7.63
//
[ok]

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

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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