Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate H281DRAFT_04953 H281DRAFT_04953 acetyl-coenzyme A synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__Burk376:H281DRAFT_04953
          Length = 660

 Score = 1120 bits (2898), Expect = 0.0
 Identities = 527/659 (79%), Positives = 593/659 (89%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MSAIESV+QE RVF P    A+ A I  M+AY AL  EAERDYEGFW R ARE L W KP
Sbjct: 1   MSAIESVLQERRVFPPSAEAAAGATISGMDAYHALTAEAERDYEGFWGRLARETLSWNKP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLD+S APFY WFEDG+LNASYN +DR+++ GN ++VAI+FEADDG+VT VTY++L 
Sbjct: 61  FTKVLDESKAPFYTWFEDGQLNASYNSIDRHVEAGNGERVAIIFEADDGTVTNVTYQDLL 120

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

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           LVDVGAVAL+T+DEQMRGGKALPLK IAD+ALA+GGCEAV++VIVY+RTGGK+AW E RD
Sbjct: 181 LVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCEAVKSVIVYQRTGGKIAWNESRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            WM ++S  + D C  E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA  TMKWTFD
Sbjct: 241 LWMHEISQAESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTMKWTFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
            K  D+FWCTADIGW+TGH+YI YGPL  G TQVVFEGVPTYPNAGRFWDMIA+HKV++F
Sbjct: 301 WKSSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVTLF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKAAEAD K+HPK YDLS+LR++GTVGEPINPEAW+WYY+N+G  RCPIV
Sbjct: 361 YTAPTAIRSLIKAAEADAKVHPKSYDLSTLRIIGTVGEPINPEAWVWYYENVGGGRCPIV 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
           GTMEIESALVSNP+VAEAAVVGRPD  TGEA+CAFVVLKR+RP GEEAVK+A ELRNWVG
Sbjct: 541 GTMEIESALVSNPIVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEAVKLANELRNWVG 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: 1583
Number of extensions: 67
Number of successful extensions: 2
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 H281DRAFT_04953 H281DRAFT_04953 (acetyl-coenzyme A 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.13963.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.6e-297  972.1   0.0   6.4e-297  971.9   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04953  H281DRAFT_04953 acetyl-coenzyme 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04953  H281DRAFT_04953 acetyl-coenzyme A synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.9   0.0  6.4e-297  6.4e-297       2     627 ..      27     657 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 971.9 bits;  conditional E-value: 6.4e-297
                                    TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhv 67 
                                                  + +++y++l++ea++d+e fw++la+e+l+w kpf+kvldes++p+++Wfedg+ln+syn++drhv
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953  27 SGMDAYHALTAEAERDYEGFWGRLARETLSWNKPFTKVLDESKAPFYTWFEDGQLNASYNSIDRHV 92 
                                                  57899************************************************************* PP

                                    TIGR02188  68 ek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviaml 132
                                                  e+ + ++vaii+e+d+ +  + ++tY++ll++v+r+an+lk+ Gvkkgdrv+iY+pm +e ++am+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953  93 EAgNGERVAIIFEADDGT--VTNVTYQDLLQRVSRFANALKTRGVKKGDRVVIYMPMSIEGIVAMQ 156
                                                  ***************664..8********************************************* PP

                                    TIGR02188 133 acaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svek 197
                                                  acaRiGa+hsvvf+Gfs+++l+eR+vd+ a  ++t+de++Rggk+++lk+i+deal++  + +v++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 157 ACARIGATHSVVFGGFSSKSLNERLVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCeAVKS 222
                                                  **********************************************************99889*** PP

                                    TIGR02188 198 vlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgG 263
                                                  v+v++rtg ++a w+e+rD+w++e+ +  +s++c+pe++++e+plfiLYtsGstGkPkGv+h+tgG
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 223 VIVYQRTGGKIA-WNESRDLWMHEISQA-ESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGG 286
                                                  **********77.*************95.************************************* PP

                                    TIGR02188 264 ylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwevi 329
                                                  yll+aa t+k++fd k +d+fwCtaD+GW+tGhsYi ygPL+ G t+++fegvptyp+a+rfw++i
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 287 YLLWAAQTMKWTFDWKSSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMI 352
                                                  ****************************************************************** PP

                                    TIGR02188 330 ekykvtifYtaPtaiRalmklg....eelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcp 391
                                                   k+kvt fYtaPtaiR+l+k++    + ++k++dls+lr++g+vGepinpeaw Wyye+vG ++cp
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 353 AKHKVTLFYTAPTAIRSLIKAAeadaKVHPKSYDLSTLRIIGTVGEPINPEAWVWYYENVGGGRCP 418
                                                  *******************9983333457899********************************** PP

                                    TIGR02188 392 ivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPs 457
                                                  ivdtwWqtetGg++itplpg at+l pgs+tlPl+Gi+a+vvde+g++v ++++ g+Lv+k+pwPs
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 419 IVDTWWQTETGGHMITPLPG-ATPLVPGSCTLPLPGIMAAVVDETGQDVPNGQG-GILVVKRPWPS 482
                                                  ********************.6*****************************999.8********** PP

                                    TIGR02188 458 mlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesa 520
                                                  mlr ++gd++r+ ++Yf +  g  ly++GDga+rdkd Gy++i+GR+Ddv+nvsGhrlgt+eiesa
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 483 MLRNVWGDPDRYKKSYFPEELGgkLYLAGDGAVRDKDtGYFTIMGRIDDVLNVSGHRLGTMEIESA 548
                                                  *****************9876567************99**************************** PP

                                    TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdkilv 584
                                                  lvs++ vaeaavvg+pd ++gea++afvvlk+++ e ee  +l++el+++v keigpiakp++i++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 549 LVSNPIVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEavKLANELRNWVGKEIGPIAKPKDIRF 614
                                                  ********************************99988887799*********************** PP

                                    TIGR02188 585 veelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                                   e+lPktRsGkimRRllr++a+gee+++dvstle+p+++++l 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04953 615 GENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENPAILDQLG 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: 00:00:00.04
# Mc/sec: 10.03
//
[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, or view the source code.

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