Alignments for a candidate for acs in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhodobacter ovatus JA234

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate WP_097030475.1 CRO07_RS09580 AMP-binding protein

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_900207575.1:WP_097030475.1
          Length = 553

 Score =  529 bits (1362), Expect = e-154
 Identities = 277/548 (50%), Positives = 340/548 (62%), Gaps = 18/548 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L K  AN+ ALTPL  L RAA V   R +++HG+   T+ + + R  RLASALA   I P
Sbjct: 10  LEKCAANFAALTPLSHLKRAAEVFTDRIALVHGATRLTYGEYHARVSRLASALAGMGIQP 69

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G  VA I PNI    EAH+GVP  GA+LN +NIRL+  TVA++  H  + +++ D  F  
Sbjct: 70  GDVVATILPNIAQQAEAHWGVPAAGAILNTINIRLDVETVAYIFDHGGAKLVLCDTAFLP 129

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           LA  +   ME K       P +I + D      +    L     EYED LA G P  PW 
Sbjct: 130 LARAACEKMEGKP------PTIIEVCDREAGHSATGEFL-----EYEDLLAKGSPWAPWV 178

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P DEW+S+AL YTSGTT  PKGVV HHRGAY+    N + W MQ   VYL  +P+FHCN
Sbjct: 179 MPEDEWESLALNYTSGTTGRPKGVVYHHRGAYLATYGNAIAWRMQLYPVYLTIVPLFHCN 238

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311
           GWC  W + +L GT +C R VTAK +Y+ IA   VTHF  AP+VLNAI+NA  ED     
Sbjct: 239 GWCHTWMVPMLGGTVVCCRDVTAKAIYAAIADEGVTHFGGAPIVLNAIINAGAEDR-RDF 297

Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
            H V V TAGA PP + L ++   GF V   YGL+E YGP+T C WKPEWD+   + +A 
Sbjct: 298 GHVVEVFTAGAPPPAATLAAIEPLGFNVTQVYGLTEVYGPATECIWKPEWDATTGDERAA 357

Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431
           L AR GV    +E  +V DT  G+P+P D    GEI  RGNMVMKGY KNPEA  E F  
Sbjct: 358 LKARTGVGMATLEGAEVHDTH-GQPIPRDTVHLGEIAMRGNMVMKGYYKNPEATAEAFKD 416

Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491
           GWF SGDIA +HPD YI+I DR+KD+IISGGEN+SSVEVE V+ HHPAV   +VVARPD+
Sbjct: 417 GWFRSGDIAFQHPDGYIKITDRAKDIIISGGENVSSVEVEGVIAHHPAVSLCAVVARPDD 476

Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551
           RW E PCAFV L     K  +     +I+ F RE+L  +  PK V+F  LPKT+TGKIQK
Sbjct: 477 RWGEVPCAFVEL-----KRGRQATEAEIIAFVRERLAGFKTPKQVIFCDLPKTSTGKIQK 531

Query: 552 HILRTKAK 559
             LR  A+
Sbjct: 532 FELRAVAR 539


Lambda     K      H
   0.319    0.134    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: 894
Number of extensions: 38
Number of successful extensions: 5
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: 569
Length of database: 553
Length adjustment: 36
Effective length of query: 533
Effective length of database: 517
Effective search space:   275561
Effective search space used:   275561
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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