Alignments for a candidate for acs in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pandoraea thiooxydans ATSB16

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_047212428.1 PATSB16_RS02175 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001931675.1:WP_047212428.1
          Length = 660

 Score = 1130 bits (2924), Expect = 0.0
 Identities = 534/660 (80%), Positives = 593/660 (89%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           M++IESVM E RVF PP+    QA I  M AYQALC EAERD+EGFWAR ARE + W KP
Sbjct: 1   MASIESVMHEQRVFAPPQALVEQANISGMAAYQALCAEAERDHEGFWARLARENVAWHKP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLDQSNAPFY WFEDG+LN SYNCLDRNLQNGNA+K AI+FEADDG+ T VTYRELH
Sbjct: 61  FTKVLDQSNAPFYTWFEDGQLNVSYNCLDRNLQNGNAEKTAIIFEADDGTSTPVTYRELH 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +VCRFAN LK+ GI+KGDRVVIYMPMS+EGVVAMQACAR+GATHSVVF GFSAKSL ER
Sbjct: 121 QRVCRFANALKSRGIKKGDRVVIYMPMSIEGVVAMQACARIGATHSVVFAGFSAKSLNER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           ++D GAVA+ITADEQMRGG+ALPLK + D+AL LGGC+A+  V+VYRRTGG      GRD
Sbjct: 181 IIDAGAVAVITADEQMRGGRALPLKNVVDEALTLGGCDALHTVVVYRRTGGPATMQAGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            WM ++SAGQ + CE E V AEHPLF+LYTSGSTGKPKGVQHS+GGYLLWA +TM+WTFD
Sbjct: 241 VWMHELSAGQSEQCEPEWVGAEHPLFILYTSGSTGKPKGVQHSSGGYLLWATLTMQWTFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           IKP D+FWCTADIGWVTGHTYIAYGPLA GATQ+VFEGVPTYPNAGRFWDMIARHKVSIF
Sbjct: 301 IKPSDVFWCTADIGWVTGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMIARHKVSIF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKAAE+D+ I+P QYDLSSLR+LG+VGEPINPEAWMWYYKN+G ERCPIV
Sbjct: 361 YTAPTAIRSLIKAAESDKSIYPTQYDLSSLRILGSVGEPINPEAWMWYYKNVGGERCPIV 420

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETGGH+I PLPG TP VPGSCTLPLPG+ AAIVDETG DVPNG GG+LV+KRPW
Sbjct: 421 DTWWQTETGGHVIAPLPGVTPQVPGSCTLPLPGVAAAIVDETGQDVPNGQGGMLVIKRPW 480

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P ++RTIWGDPERF+ SYFP ELGGK+YLAGDG+IRD+ TGYFTIMGRIDDVLNVSGHR+
Sbjct: 481 PGLLRTIWGDPERFKNSYFPAELGGKIYLAGDGAIRDRQTGYFTIMGRIDDVLNVSGHRL 540

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALV+NPLVAEAAVVGRPDD TGEA+ AFVVLKR+RP GEEA +IAT+LRNWV 
Sbjct: 541 GTMEIESALVANPLVAEAAVVGRPDDTTGEAVVAFVVLKRARPGGEEAKQIATDLRNWVA 600

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660
           KEIGPIAKP+DIRFG+NLPKTRSGKIMRRLLR +AKGEEITQDTSTLENPAILEQLKQ+Q
Sbjct: 601 KEIGPIAKPRDIRFGENLPKTRSGKIMRRLLRVIAKGEEITQDTSTLENPAILEQLKQSQ 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: 1531
Number of extensions: 63
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 WP_047212428.1 PATSB16_RS02175 (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.3188070.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-301  984.6   0.0     1e-300  984.4   0.0    1.0  1  NCBI__GCF_001931675.1:WP_047212428.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001931675.1:WP_047212428.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  984.4   0.0    1e-300    1e-300       3     628 ..      28     658 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 984.4 bits;  conditional E-value: 1e-300
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                            + +y++l++ea++d+e fwa+la+e+++w+kpf+kvld+s++p+++Wfedg+lnvsync+dr++++ +++k+
  NCBI__GCF_001931675.1:WP_047212428.1  28 GMAAYQALCAEAERDHEGFWARLARENVAWHKPFTKVLDQSNAPFYTWFEDGQLNVSYNCLDRNLQNgNAEKT 100
                                           6789********************************************************************* PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aii+e+d+ +  s  +tY+el+++vcr+an+lk+ G+kkgdrv+iY+pm +e v+am+acaRiGa+hsvvfaG
  NCBI__GCF_001931675.1:WP_047212428.1 101 AIIFEADDGT--STPVTYRELHQRVCRFANALKSRGIKKGDRVVIYMPMSIEGVVAMQACARIGATHSVVFAG 171
                                           *******765..79*********************************************************** PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvww 219
                                           fsa++l+eRi+da a  vitade++Rgg++++lk++vdeal+   + ++++v+v++rtg + a+++ grDvw+
  NCBI__GCF_001931675.1:WP_047212428.1 172 FSAKSLNERIIDAGAVAVITADEQMRGGRALPLKNVVDEALTLGGCdALHTVVVYRRTGGP-ATMQAGRDVWM 243
                                           *****************************************9988879*************.66********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           +el + ++s++cepe++++e+plfiLYtsGstGkPkGv+h++gGyll+a+lt++++fdik++d+fwCtaD+GW
  NCBI__GCF_001931675.1:WP_047212428.1 244 HELSA-GQSEQCEPEWVGAEHPLFILYTSGSTGKPKGVQHSSGGYLLWATLTMQWTFDIKPSDVFWCTADIGW 315
                                           *****.6****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee....lvkkhdls 361
                                           vtGh+Yi ygPLa+Gat+++fegvptyp+a+rfw++i ++kv+ifYtaPtaiR+l+k++e+     ++++dls
  NCBI__GCF_001931675.1:WP_047212428.1 316 VTGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAESdksiYPTQYDLS 388
                                           *********************************************************996522335789**** PP

                             TIGR02188 362 slrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd 434
                                           slr+lgsvGepinpeaw+Wyy++vG e+cpivdtwWqtetGg++i+plpg +t++ pgs+tlPl+G+ a++vd
  NCBI__GCF_001931675.1:WP_047212428.1 389 SLRILGSVGEPINPEAWMWYYKNVGGERCPIVDTWWQTETGGHVIAPLPG-VTPQVPGSCTLPLPGVAAAIVD 460
                                           **************************************************.5********************* PP

                             TIGR02188 435 eegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdv 504
                                           e+g++v ++++ g+Lvik+pwP++lrti+gd+erf ++Yf +  g  +y++GDga rd++ Gy++i+GR+Ddv
  NCBI__GCF_001931675.1:WP_047212428.1 461 ETGQDVPNGQG-GMLVIKRPWPGLLRTIWGDPERFKNSYFPAELGgkIYLAGDGAIRDRQtGYFTIMGRIDDV 532
                                           ********999.8***************************9766567***********766************ PP

                             TIGR02188 505 invsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigp 575
                                           +nvsGhrlgt+eiesalv+++ vaeaavvg+pd+++gea+vafvvlk+++   ee  +++++l+++v+keigp
  NCBI__GCF_001931675.1:WP_047212428.1 533 LNVSGHRLGTMEIESALVANPLVAEAAVVGRPDDTTGEAVVAFVVLKRARPGGEEakQIATDLRNWVAKEIGP 605
                                           ***********************************************99985555459*************** PP

                             TIGR02188 576 iakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           iakp++i++ e+lPktRsGkimRRllr ia+gee+++d+stle+p+++e+lk+
  NCBI__GCF_001931675.1:WP_047212428.1 606 IAKPRDIRFGENLPKTRSGKIMRRLLRVIAKGEEITQDTSTLENPAILEQLKQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 26.48
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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