Alignments for a candidate for acs in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Collimonas arenae Ter10

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_061534290.1 CAter10_RS16665 propionate--CoA ligase

Query= curated2:Q9RRL7
         (649 letters)



>NCBI__GCF_001584165.1:WP_061534290.1
          Length = 630

 Score =  475 bits (1222), Expect = e-138
 Identities = 271/627 (43%), Positives = 384/627 (61%), Gaps = 29/627 (4%)

Query: 39  YRQSLDQPDDFWSEVAHDLHWMKDWDRVLD-WQEPHAQWFVGGQTNIAYNALDRNVQRGL 97
           Y++S+D P  FW E A  + W   + +VLD  + P A+WFVGG TN+ +NA+DR V    
Sbjct: 7   YQRSIDDPSAFWREQARRIDWHHPFSQVLDDSRPPFAKWFVGGTTNLCHNAVDRWVGTRG 66

Query: 98  GDKRAIIWEGEDGEVRTYTYAELLREVCKAANALEELGVVAGDRVTLYMPLIPEAAIAML 157
                I    E    +TY++ EL  EV + A  ++ LGV  GDRV +YMP+I EA  AML
Sbjct: 67  EQPALIAISTETNTEKTYSFRELQDEVIRTAAIMQSLGVGRGDRVLIYMPMIAEATFAML 126

Query: 158 ACARIGAVHSIVFGGFSVSALADRINNAQSKLLITADAGYRRGKPVTLKINADEAAKLAP 217
           ACARIGA+HS+VFGGF+ ++LA RI++AQ  L+++ADAG R GK V  K   D+A KLA 
Sbjct: 127 ACARIGAIHSVVFGGFASNSLASRIDDAQPVLIVSADAGSRGGKVVPYKGLLDDAIKLAQ 186

Query: 218 CLE-HVLVVKRAGIPLEWWTEGRDLWWHDVVDRQSDQHEATA----LDSEHPLFILYTSG 272
               HVL+V R   P+E    GRD+   D  + +    +A      L+S    +ILYTSG
Sbjct: 187 HKPAHVLLVDRGLAPMEM-VAGRDV---DYAEHRRLHIDAKVPVVWLESNEASYILYTSG 242

Query: 273 STGAPKGVQHTTGGYMVGTYLTTQTVFDLRDDDIYWCTADIGWITGHSYSVYGPLLNGAT 332
           +TG PKGVQ   GGY V    +   +F  +    Y+CT+DIGW+ GHSY VYGPL+ G  
Sbjct: 243 TTGKPKGVQRDVGGYAVALATSMDAIFCGKPGGTYFCTSDIGWVVGHSYIVYGPLIAGMA 302

Query: 333 VVMYEGAPNQPDWGRFWDIVQKHRVTILYTAPTAIRSFMQHGDEIPGRYDLASLRLLGSV 392
            V+YEG P +PD G +W IV+K++VT +++APTAIR   +   E+  +YDL+SL+ L   
Sbjct: 303 TVLYEGLPIRPDAGIWWSIVEKYKVTRMFSAPTAIRVLKKQPPELMKKYDLSSLQALYLA 362

Query: 393 GEPINPEAWMWYYRVIGGERCPVVDTWWQTETGSIMLTTLPGA--FPSKPGSAGLPMFGV 450
           GEP++     W    +G    P+VD +WQTE+G  +LT        P K GS G+PM+G 
Sbjct: 363 GEPLDETTSSWISEALG---VPIVDNYWQTESGWPILTIAKNIEDKPCKLGSPGVPMYGY 419

Query: 451 EPALMTR-DGEEIGDDDGGLLVIKRPW-PSMLRTVYGDDERYRKSYW-GEIPH----VYF 503
           +  L+    G   G ++ G++VI+ P  P  ++T+YGDD R+  +YW  + P     +Y 
Sbjct: 420 KVRLLNEATGALCGANEKGVVVIEGPLPPGCMQTIYGDDRRFVDTYWTTQSPESGRPMYS 479

Query: 504 AGDGARRDHDGYYTIVGRVDDVLNVSGHRLGTMEIESALVAHPDVSEAAVVGRPDPVKGE 563
             D   RD DGYY I+GR DDV+NV+GHRLGT EIE ++ +HP+VSE AVVG  D +KG+
Sbjct: 480 TFDWGIRDDDGYYFILGRTDDVINVAGHRLGTREIEESISSHPNVSEVAVVGVEDKLKGQ 539

Query: 564 SVVAYVL--LQDGHTADPAALRAH----VSSEIGALARPDAIYIADALPKTRSGKIMRRF 617
             VA+V+  + D  T   A L A     V  +IG++ RP  +Y+   LPKTRSGK++RR 
Sbjct: 540 VAVAFVIPKVADNTTKGRATLEAEIMRVVDKQIGSVGRPARVYVVGLLPKTRSGKLLRRS 599

Query: 618 LRQLAAGQPVQGDTSTLEDPTVLERLQ 644
           ++ +  G+   GD +T+EDP+ L++++
Sbjct: 600 IQAICEGRD-PGDLTTIEDPSSLQQIK 625


Lambda     K      H
   0.319    0.137    0.432 

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: 1208
Number of extensions: 67
Number of successful extensions: 10
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: 649
Length of database: 630
Length adjustment: 38
Effective length of query: 611
Effective length of database: 592
Effective search space:   361712
Effective search space used:   361712
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: 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