Alignments for a candidate for acs in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Herbaspirillum seropedicae SmR1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate HSERO_RS07770 HSERO_RS07770 acetyl-CoA synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__HerbieS:HSERO_RS07770
          Length = 660

 Score = 1112 bits (2877), Expect = 0.0
 Identities = 518/657 (78%), Positives = 592/657 (90%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IE+  QE+RVF PP      AAI  M+AY AL  E  +DYEG WAR A++ L W KPFT+
Sbjct: 4   IETFKQENRVFAPPAELVKHAAISGMDAYHALNAEFAKDYEGTWARLAKDNLKWHKPFTQ 63

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
            LD+SNAPFYKWF DG++N SYNCLD NL+NGNADK A++FE+DDG VTRV+YRELH KV
Sbjct: 64  TLDESNAPFYKWFADGQVNVSYNCLDVNLENGNADKTAVIFESDDGKVTRVSYRELHQKV 123

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           C+FANGLK+LGI+KGDRVVIYMPMSVEGV AMQACAR+GATHSVVFGGFSAKSL ER++D
Sbjct: 124 CQFANGLKSLGIKKGDRVVIYMPMSVEGVAAMQACARIGATHSVVFGGFSAKSLHERVID 183

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
            GAVA++TAD Q+RGGK LPLK+I D+AL +GGC+ +++V+VY+R G ++ W EGRD W+
Sbjct: 184 AGAVAVLTADYQVRGGKQLPLKSIVDEALDMGGCDTLKHVVVYKRAGAEINWVEGRDLWL 243

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            DV A Q DTCE E V AEHPLF+LYTSGSTGKPKGVQH++ GYLLWA++TMKWTFDIKP
Sbjct: 244 SDVVANQSDTCEPEWVDAEHPLFILYTSGSTGKPKGVQHASAGYLLWAVLTMKWTFDIKP 303

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
           DD++WCTADIGW+TGHTYIAYGPLA GATQ+VFEGVPTYPNAGRFWDM+ARHK +IFYTA
Sbjct: 304 DDVYWCTADIGWITGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMVARHKATIFYTA 363

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTAIRSLIKAA+ADEK+HPKQYDLSSLR+LG+VGEPINPEAWMWYYKN+G+E CPIVDTF
Sbjct: 364 PTAIRSLIKAADADEKVHPKQYDLSSLRILGSVGEPINPEAWMWYYKNVGHENCPIVDTF 423

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETGGHMI+PLPGATP VPGSCTLPLPGI AAIVDETG+D+PNGNGGILVVKRPWP+M
Sbjct: 424 WQTETGGHMISPLPGATPQVPGSCTLPLPGITAAIVDETGNDIPNGNGGILVVKRPWPSM 483

Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543
           IRTIW DPERF+KSYFPEELGGK+YLAGDG++R+K+TGYFTI GRIDDVLNVSGHRMGTM
Sbjct: 484 IRTIWNDPERFKKSYFPEELGGKIYLAGDGAVRNKETGYFTITGRIDDVLNVSGHRMGTM 543

Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603
           EIESALV+N +VAEAAVVG+PD+ TGE+ICAFVVLKR RPTG+EA +IA ELR+WV KEI
Sbjct: 544 EIESALVANSIVAEAAVVGKPDETTGESICAFVVLKRPRPTGDEAKQIAKELRDWVAKEI 603

Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660
           GPIAKPK+IRFGDNLPKTRSGKIMRRLLR LAKGE ITQD STLENPAIL+QLK+AQ
Sbjct: 604 GPIAKPKEIRFGDNLPKTRSGKIMRRLLRVLAKGEAITQDVSTLENPAILDQLKEAQ 660


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: 1529
Number of extensions: 64
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 HSERO_RS07770 HSERO_RS07770 (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.28783.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   9.4e-297  971.3   0.0   1.1e-296  971.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS07770  HSERO_RS07770 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS07770  HSERO_RS07770 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.1   0.0  1.1e-296  1.1e-296       2     628 ..      27     658 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 971.1 bits;  conditional E-value: 1.1e-296
                                  TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek 69 
                                                + +++y++l +e ++d+e  wa+lak++l+w+kpf+++ldes++p++kWf+dg++nvsync+d ++e+
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770  27 SGMDAYHALNAEFAKDYEGTWARLAKDNLKWHKPFTQTLDESNAPFYKWFADGQVNVSYNCLDVNLEN 94 
                                                57899*************************************************************** PP

                                  TIGR02188  70 .rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaR 136
                                                 ++dk+a+i+e+d+ +  + +++Y+el+++vc++an lk+lG+kkgdrv+iY+pm +e v+am+acaR
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770  95 gNADKTAVIFESDDGK--VTRVSYRELHQKVCQFANGLKSLGIKKGDRVVIYMPMSVEGVAAMQACAR 160
                                                *************664..89************************************************ PP

                                  TIGR02188 137 iGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkr 203
                                                iGa+hsvvf+Gfsa++l+eR++da a  v+tad ++Rggk+++lk+ivdeal++  + ++++v+v+kr
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 161 IGATHSVVFGGFSAKSLHERVIDAGAVAVLTADYQVRGGKQLPLKSIVDEALDMGGCdTLKHVVVYKR 228
                                                ******************************************************99889********* PP

                                  TIGR02188 204 tgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaalt 271
                                                +g+e++ w+egrD+w++++v+ ++s++cepe++d+e+plfiLYtsGstGkPkGv+h+++Gyll+a+lt
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 229 AGAEIN-WVEGRDLWLSDVVA-NQSDTCEPEWVDAEHPLFILYTSGSTGKPKGVQHASAGYLLWAVLT 294
                                                ****66.**************.5********************************************* PP

                                  TIGR02188 272 vkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYt 339
                                                +k++fdik++d++wCtaD+GW+tGh+Yi ygPLa+Gat+++fegvptyp+a+rfw+++ ++k tifYt
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 295 MKWTFDIKPDDVYWCTADIGWITGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMVARHKATIFYT 362
                                                ******************************************************************** PP

                                  TIGR02188 340 aPtaiRalmklgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGg 403
                                                aPtaiR+l+k++++    ++k++dlsslr+lgsvGepinpeaw+Wyy++vG+e+cpivdt+WqtetGg
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 363 APTAIRSLIKAADAdekvHPKQYDLSSLRILGSVGEPINPEAWMWYYKNVGHENCPIVDTFWQTETGG 430
                                                **********985422337899********************************************** PP

                                  TIGR02188 404 ilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfve 471
                                                ++i+plpg at++ pgs+tlPl+Gi+a++vde+g+++ ++++ g+Lv+k+pwPsm+rti++d+erf +
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 431 HMISPLPG-ATPQVPGSCTLPLPGITAAIVDETGNDIPNGNG-GILVVKRPWPSMIRTIWNDPERFKK 496
                                                ********.6*****************************999.8************************ PP

                                  TIGR02188 472 tYfkklkg..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvp 536
                                                +Yf +  g  +y++GDga+r+k+ Gy++i+GR+Ddv+nvsGhr+gt+eiesalv+++ vaeaavvg+p
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 497 SYFPEELGgkIYLAGDGAVRNKEtGYFTITGRIDDVLNVSGHRMGTMEIESALVANSIVAEAAVVGKP 564
                                                ***9876567*********99877******************************************** PP

                                  TIGR02188 537 deikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllr 602
                                                de++ge+i+afvvlk+ + + +e  +++kel+++v+keigpiakp++i++ ++lPktRsGkimRRllr
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 565 DETTGESICAFVVLKRPRPTGDEakQIAKELRDWVAKEIGPIAKPKEIRFGDNLPKTRSGKIMRRLLR 632
                                                ***************99987776669****************************************** PP

                                  TIGR02188 603 kiaegeellgdvstledpsvveelke 628
                                                 +a+ge +++dvstle+p+++++lke
  lcl|FitnessBrowser__HerbieS:HSERO_RS07770 633 VLAKGEAITQDVSTLENPAILDQLKE 658
                                                ***********************997 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 8.04
//
[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