Alignments for a candidate for acs in Thermomonospora curvata DSM 43183

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Thermomonospora curvata DSM 43183

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_012852611.1 TCUR_RS11195 AMP-dependent synthetase and ligase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000024385.1:WP_012852611.1
          Length = 479

 Score =  321 bits (823), Expect = 4e-92
 Identities = 184/484 (38%), Positives = 265/484 (54%), Gaps = 25/484 (5%)

Query: 65  SVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDK 124
           S+ DP RFWG AA ++ W  P  + L++  PP   WF  G LN+C NA+DRH+  G GD+
Sbjct: 11  SITDPARFWGMAAREVHWLVPPDRVLDDGAPPFYRWFTGGELNVCDNALDRHVAAGHGDR 70

Query: 125 IAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLAC 184
            A+IY           ++ E+ E V++ AG L + GV  GD V++++P+ P A+ A+LAC
Sbjct: 71  PALIYPGGAAGPPQVRTFGELAETVARFAGALAELGVGGGDRVLVHLPLSPDAVVAVLAC 130

Query: 185 ARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHK 244
           AR+GA+H +      + EL+ +ID  +PK VV A+     G      P+LE ALR+  H+
Sbjct: 131 ARLGAVHVVPSQRAGAGELAAQIDLTRPKAVVAAA-----GEDGTAKPVLESALRLASHR 185

Query: 245 PDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKG 304
             R LI +RP+   VP    RD+ WEE +A A+   C P  +  PL+IL+  G  G+ +G
Sbjct: 186 IPRRLIRHRPDARVVP---PRDVTWEEALAAARPAGCAPAAATDPLHILFAPGPEGVVRG 242

Query: 305 VVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGK 364
           VVR  GGYAV L WTM  IYG  PGEV+ A  DLGW  G S   + PLL G T +L++G 
Sbjct: 243 VVRDHGGYAVALRWTMEHIYGAGPGEVFGATCDLGWAAGLSGALHAPLLTGCTLLLHDG- 301

Query: 365 PVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERC 424
                    ++   AEHG  A+ T      A+R    G A  +  +      +F+AG R 
Sbjct: 302 ------GAGFWAAAAEHGAKAVLTTAATAGALRA--AGGAPDRAPA-----AVFLAGRRP 348

Query: 425 DVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTP-PPGQAGKCVPGYNVMIL 483
           D      + +    PV   W + ETG PI A+  GL    TP  P  AG  VPG++V +L
Sbjct: 349 DRRICARASRALCRPVTWQWERPETGRPIAAAPHGL--EPTPVDPEAAGPPVPGFDVHVL 406

Query: 484 DDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEG 543
             +     A + G + ++LPLPPG+ + LW++ E F   +  + PGY+ T DAG +  +G
Sbjct: 407 APDGAPAAAGTDGELAIRLPLPPGSLTTLWRDDERFVAEHLARRPGYFLTGDAGRLGADG 466

Query: 544 YLYV 547
           ++ V
Sbjct: 467 HVRV 470


Lambda     K      H
   0.318    0.136    0.421 

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: 1034
Number of extensions: 69
Number of successful extensions: 6
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: 683
Length of database: 479
Length adjustment: 36
Effective length of query: 647
Effective length of database: 443
Effective search space:   286621
Effective search space used:   286621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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