Alignments for a candidate for acs in Luteimonas huabeiensis HB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Luteimonas huabeiensis HB2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_024891196.1 Z164_RS0113385 propionate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_000559025.1:WP_024891196.1
          Length = 629

 Score =  481 bits (1237), Expect = e-140
 Identities = 262/637 (41%), Positives = 391/637 (61%), Gaps = 19/637 (2%)

Query: 30  IDAYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVD 89
           +  Y + +R+++E  E+FW   A+ + W +P +++LD SNPP  KWFVGG  NL Y AVD
Sbjct: 1   MSTYEEVYRRSIEQPEAFWAEEARAIHWHRPPERILDDSNPPLRKWFVGGETNLCYNAVD 60

Query: 90  RHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKI 149
           RH++  R ++LA+      V  +      R++TY  L+REVN  A  L +   V +GD++
Sbjct: 61  RHLQA-RGDQLAL------VAVSTETGATREITYRQLHREVNAFAAALLR-LDVGRGDRV 112

Query: 150 TLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRV 209
            +Y+P + E    MLA  RIGAI SVVF GF+A  LA RI+D++ ++++ AD   R GR+
Sbjct: 113 VIYMPNMAEAVFAMLACARIGAIHSVVFGGFAAHNLALRIDDAEPKLLVCADAGSRGGRI 172

Query: 210 VRLKEVVDAALEKATGVESVIVLPRLGLKDV-PMTEGRDYWWNKLMQGIPPNAYIEPEPV 268
           +  K +VD A  +A      +++   GL    P   GRD  + +L +     A +    +
Sbjct: 173 IPYKPLVDEACARAKSPPPHVLIVSRGLDPAEPRVAGRDVDYAEL-RAQTGEAEVPVAWL 231

Query: 269 ESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGH 328
           ES  PS++LYTSGTTGKPKG+  D GG+AV +  +M+ +FD     + + T+D+GW  GH
Sbjct: 232 ESNEPSYLLYTSGTTGKPKGVQRDVGGYAVAMAQSMRTIFDCAPGQVMFSTSDVGWAVGH 291

Query: 329 SYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPR 388
           SY V GPL+ G T ++YEG P  P P  WWS+ ERYGV   ++SPTAIR+  ++   + R
Sbjct: 292 SYNVYGPLIGGCTSLLYEGLPVNPDPGIWWSLCERYGVGTLFSSPTAIRVLKKHDVSYLR 351

Query: 389 KHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVP 448
           + DLS L  +   GEP++    RW    LG   +     +W TETG   ++  PGL + P
Sbjct: 352 ERDLSKLEYLFLAGEPLDEPTARWISAALGKPVI---DNYWQTETGWPALTLMPGLDMKP 408

Query: 449 MKPGTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYW 506
           ++ G+ G P  G+ + VV E +G    P  KG LVI+ P  PG +  IW D  R++ +Y+
Sbjct: 409 VRFGSPGFPNLGYRMKVVREGSGETVGPNEKGVLVIEPPLPPGCMSTIWRDDRRFLDSYF 468

Query: 507 SRFPGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVV 565
           S F  + Y+  D+A++D+DGY ++LGR D+VI VAGHRLGT E+E A+ S PAVAE+AVV
Sbjct: 469 SHFNELLYSSLDWAVRDEDGYTFILGRTDDVINVAGHRLGTREIEEAVSSCPAVAEAAVV 528

Query: 566 GVPDAIKGEVPIAFVVLKQ---GVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKT 622
           GV D +KG+VPI F  L+      A  ++  ++++  V  ++G +A PA++  V  LPKT
Sbjct: 529 GVADELKGQVPIVFATLRDPGADAAAREQAARDMQRAVDASLGAVARPARVHVVGALPKT 588

Query: 623 RSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659
           RSGK++RR L+A+A G   GD++TL+D  +++E +RA
Sbjct: 589 RSGKLLRRSLQALAEGRDPGDLSTLDDPGALDEIRRA 625


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: 1269
Number of extensions: 82
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: 629
Length adjustment: 38
Effective length of query: 632
Effective length of database: 591
Effective search space:   373512
Effective search space used:   373512
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 Sep 24 2021. 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