Alignments for a candidate for acs in Rhodanobacter denitrificans FW104-10B01

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhodanobacter denitrificans FW104-10B01

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_255326666.1 LRK54_RS00715 propionate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_021560695.1:WP_255326666.1
          Length = 648

 Score =  505 bits (1300), Expect = e-147
 Identities = 274/640 (42%), Positives = 401/640 (62%), Gaps = 17/640 (2%)

Query: 27  YTPIDAYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYL 86
           ++P   Y  F+RQ+++  E FW   A+ + W  P  ++LD SNPPF +WFVGG  NL Y 
Sbjct: 15  WSPPMRYEDFYRQSIDEPEQFWAEQARLIHWHVPPRQILDQSNPPFRRWFVGGTTNLCYN 74

Query: 87  AVDRHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKG 146
           A+DRH+   R  +LA+      V  +      R+ TY  L+REVN  A +L Q+ GV KG
Sbjct: 75  AIDRHLAE-RPEQLAL------VAISSETGITREFTYRQLHREVNTFAAVL-QSLGVGKG 126

Query: 147 DKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRR 206
           D++ +YLP + E    MLA  RIGAI SVVF GF+A  LA RI+D+Q ++++ AD   R 
Sbjct: 127 DRVVIYLPNIAEAVFAMLACARIGAIHSVVFGGFAAHNLALRIDDAQPKLLVCADAGMRA 186

Query: 207 GRVVRLKEVVDAALEKATGVES-VIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEP 265
           G+V+  K +VDAAL++A+     V+++ R     +    GRD  + +L +    +A +  
Sbjct: 187 GKVIPYKPLVDAALDEASAPPPHVLIVDRKLDPQMTRVAGRDLDYAEL-RAQHEDAEVPV 245

Query: 266 EPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWV 325
             +ES  PS++LYTSGTTGKPKG+  D GG+AV +  +++ VFDI    + + T+D+GW 
Sbjct: 246 VWLESNEPSYLLYTSGTTGKPKGVQRDVGGYAVAMALSIRTVFDIAPGQVMFATSDVGWA 305

Query: 326 TGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEE 385
            GHSY V GPL+ GAT ++YEG P  P    WW + ERY V   ++SPTAIR+  +  E 
Sbjct: 306 VGHSYNVYGPLIGGATSLLYEGLPTRPDAGIWWQLCERYKVRTMFSSPTAIRVLKKQDES 365

Query: 386 WPRKHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLY 445
           W +K+DLS L+ +   GEP++    +W    LG   V     +W TETG   I+  PGL 
Sbjct: 366 WLKKYDLSKLKWLFLAGEPLDEPTAQWITTALG---VPVIDNYWQTETGWPAITLMPGLE 422

Query: 446 LVPMKPGTNGPPLPGFEVDVVDEN-GNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIK 503
           L  +K G+ G P PG+ + V+DEN G   P G KG LV + P  PG L  +W D +RY+ 
Sbjct: 423 LKTVKFGSPGLPAPGYRMKVIDENTGKEVPAGSKGVLVFQLPLPPGCLTTVWRDDDRYVH 482

Query: 504 TYWSRFPGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAES 562
           +Y+S F  + Y+  D+A++D+DGY +VLGR D+VI VAGHRLGT E+E ++ SHPAVAE+
Sbjct: 483 SYFSHFRELLYSSLDWAVRDEDGYTFVLGRTDDVINVAGHRLGTREIEESVASHPAVAEA 542

Query: 563 AVVGVPDAIKGEVPIAFVVLKQGVAP-SDELRKELREHVRRTIGPIAEPAQIFFVTKLPK 621
           AV+GV D +KG+VPI F  LKQ     +  + + +++ V   +G +A+P++++ V  LPK
Sbjct: 543 AVIGVKDELKGQVPIVFATLKQDAGDGAHAVAQAMQQRVVDQLGGVAKPSRVYVVNALPK 602

Query: 622 TRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYE 661
           TRSGK++RR L+A+A     GD++TL+D  ++++ +RA E
Sbjct: 603 TRSGKLLRRSLQALAEQRDPGDLSTLDDPGALDDIRRALE 642


Lambda     K      H
   0.319    0.138    0.440 

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: 1361
Number of extensions: 84
Number of successful extensions: 9
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: 670
Length of database: 648
Length adjustment: 38
Effective length of query: 632
Effective length of database: 610
Effective search space:   385520
Effective search space used:   385520
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)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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