GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Alicycliphilus denitrificans K601

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013518028.1 ALIDE2_RS18585 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000204645.1:WP_013518028.1
          Length = 665

 Score = 1069 bits (2764), Expect = 0.0
 Identities = 508/660 (76%), Positives = 581/660 (88%), Gaps = 5/660 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           SAIESV+ E+RVF PPEG    A I  M  Y+ALC EA++D+EGFWAR ARE L WT+PF
Sbjct: 6   SAIESVLIENRVFPPPEGLVKTARISGMAGYEALCAEADKDFEGFWARLARENLQWTRPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
           TK LD+SNAPFY+WF DGELNAS NCLDR++      K AI+FEADDG+VT+VTY+EL  
Sbjct: 66  TKTLDESNAPFYQWFADGELNASANCLDRHMGTPVESKTAIIFEADDGAVTKVTYKELLA 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V +FAN LKA G++KGDRV+IYMPM++EGVVAMQACAR+GATHSVVFGGFSAK++QER+
Sbjct: 126 RVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKAVQERI 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT--EGR 239
           +D GAVA+ITA+ Q+RGGK LPLKAI D+ +A+GGCE++++V+VY RT    AW   +GR
Sbjct: 186 IDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCESIKSVLVYERT--PTAWNRVDGR 243

Query: 240 DRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299
           D+   +  AGQ   C    V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA +TM WTF
Sbjct: 244 DKSFAEALAGQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTF 303

Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359
           D++PDD+FWCTADIGWVTGHTYIAYGPLAAG TQV+FEG+PTYPNAGRFW MI RHKVSI
Sbjct: 304 DLRPDDVFWCTADIGWVTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSI 363

Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419
           FYTAPTAIRSLIKAA++DEK+HPK +DLSSLR+LG+VGEPINPEAWMWYYKN+G ERCPI
Sbjct: 364 FYTAPTAIRSLIKAADSDEKVHPKNWDLSSLRILGSVGEPINPEAWMWYYKNVGGERCPI 423

Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRP 479
           VDT+WQTE GGH+ITPLPGATPLVPGSCTLPLPGI AAIVDETG DVPNG+GG+LV+KRP
Sbjct: 424 VDTWWQTENGGHLITPLPGATPLVPGSCTLPLPGIAAAIVDETGKDVPNGSGGMLVIKRP 483

Query: 480 WPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539
           WP+MIRTIW DPERF+KSYFPEE+GGK+YLAGDG++RD  T YF + GRIDDVLNVSGHR
Sbjct: 484 WPSMIRTIWNDPERFKKSYFPEEMGGKIYLAGDGAVRDAKTAYFRVTGRIDDVLNVSGHR 543

Query: 540 MGTMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598
           MGTMEIESALV+ + LVAEAAVVGRPDD+TGEAICAFVVLKR+RPTGEEA +IA ELRNW
Sbjct: 544 MGTMEIESALVAKSDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEAKQIAAELRNW 603

Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           V KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGE ITQDTSTLENPAIL+QL Q
Sbjct: 604 VAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 663


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: 1552
Number of extensions: 69
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: 665
Length adjustment: 38
Effective length of query: 622
Effective length of database: 627
Effective search space:   389994
Effective search space used:   389994
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 WP_013518028.1 ALIDE2_RS18585 (acetate--CoA ligase)
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.3993558.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-288  943.1   0.0   3.6e-288  942.9   0.0    1.0  1  NCBI__GCF_000204645.1:WP_013518028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204645.1:WP_013518028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  942.9   0.0  3.6e-288  3.6e-288       3     628 ..      32     663 ..      30     664 .. 0.96

  Alignments for each domain:
  == domain 1  score: 942.9 bits;  conditional E-value: 3.6e-288
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                            +  y++l++ea +d e fwa+la+e+l+w++pf+k+ldes++p+++Wf+dgeln+s+nc+drh+ +  + k+
  NCBI__GCF_000204645.1:WP_013518028.1  32 GMAGYEALCAEADKDFEGFWARLARENLQWTRPFTKTLDESNAPFYQWFADGELNASANCLDRHMGTpVESKT 104
                                           56789**************************************************************999*** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aii+e+d+    + k+tY+ell++v+++an+lk++Gvkkgdrv iY+pm++e v+am+acaRiGa+hsvvf+G
  NCBI__GCF_000204645.1:WP_013518028.1 105 AIIFEADDGA--VTKVTYKELLARVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGG 175
                                           *******664..8************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvww 219
                                           fsa+a++eRi+da a  vita+ +lRggk ++lk+ivde +++  + s+++vlv++rt +   + ++grD+ +
  NCBI__GCF_000204645.1:WP_013518028.1 176 FSAKAVQERIIDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCeSIKSVLVYERTPTA-WNRVDGRDKSF 247
                                           *****************************************9998889***********99.5599******* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                            e+++ ++s+ec p ++++e+plfiLYtsGstGkPkGv+h+tgGyll+a+lt+ ++fd++++d+fwCtaD+GW
  NCBI__GCF_000204645.1:WP_013518028.1 248 AEALA-GQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTFDLRPDDVFWCTADIGW 319
                                           *****.6****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee....lvkkhdls 361
                                           vtGh+Yi ygPLa+G t+++feg+ptyp+a+rfw++ie++kv+ifYtaPtaiR+l+k++++    ++k+ dls
  NCBI__GCF_000204645.1:WP_013518028.1 320 VTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSIFYTAPTAIRSLIKAADSdekvHPKNWDLS 392
                                           *********************************************************9954223378899*** PP

                             TIGR02188 362 slrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd 434
                                           slr+lgsvGepinpeaw+Wyy++vG e+cpivdtwWqte Gg+litplpg at+l pgs+tlPl+Gi a++vd
  NCBI__GCF_000204645.1:WP_013518028.1 393 SLRILGSVGEPINPEAWMWYYKNVGGERCPIVDTWWQTENGGHLITPLPG-ATPLVPGSCTLPLPGIAAAIVD 464
                                           **************************************************.6********************* PP

                             TIGR02188 435 eegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdv 504
                                           e+gk+v ++++ g+Lvik+pwPsm+rti++d+erf ++Yf +  g  +y++GDga+rd+   y+ ++GR+Ddv
  NCBI__GCF_000204645.1:WP_013518028.1 465 ETGKDVPNGSG-GMLVIKRPWPSMIRTIWNDPERFKKSYFPEEMGgkIYLAGDGAVRDAKtAYFRVTGRIDDV 536
                                           ********999.8***************************9877667***********76489********** PP

                             TIGR02188 505 invsGhrlgtaeiesalvsh.eavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeig 574
                                           +nvsGhr+gt+eiesalv++ + vaeaavvg+pd+++geai+afvvlk+++ + ee  ++++el+++v+keig
  NCBI__GCF_000204645.1:WP_013518028.1 537 LNVSGHRMGTMEIESALVAKsDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEakQIAAELRNWVAKEIG 609
                                           ******************872579*************************9987666669************** PP

                             TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           piakp++i++ ++lPktRsGkimRRllr++a+ge +++d+stle+p+++++l +
  NCBI__GCF_000204645.1:WP_013518028.1 610 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 663
                                           **************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 28.93
//
[ok]

This GapMind analysis is from Apr 09 2024. 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