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.9266.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: 8.01
//
[ok]

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

Links

Downloads

Related tools

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