GapMind for catabolism of small carbon sources

 

Alignments 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.22731.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.90
//
[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:

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:

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:

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:

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