Alignments for a candidate for hcl in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcl in Geotalea uraniireducens Rf4

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_011938514.1 GURA_RS08185 acetate--CoA ligase

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000016745.1:WP_011938514.1
          Length = 584

 Score =  170 bits (431), Expect = 1e-46
 Identities = 147/494 (29%), Positives = 233/494 (47%), Gaps = 22/494 (4%)

Query: 50  YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109
           +T+ +L  + +R  + L+  LG++  +RV V            LG +K   V   + +  
Sbjct: 80  FTFCDLKEQSSRFANVLKR-LGVEKGERVFVLAGRIPPLYIAALGCLKNISVFCPLFSAF 138

Query: 110 TESDYEYMLTDSAARVAVVSQ-ELLPLFAPMLGKVPTLEHLVVAGGAGED------SLAA 162
                   L+   AR+ V ++ +     A +   +P L H+++     +D      SL  
Sbjct: 139 GPDPIRQRLSRGDARLLVTTERQYAKKIAGIRESLPQLRHVLLTD-IDDDLDETVLSLPR 197

Query: 163 LLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGD 222
           L+A  S  F   PT P+D     ++SG+TG PKG V +H D + T  +  R ++     D
Sbjct: 198 LMAEASADFTIPPTDPEDMAVLHFTSGTTGMPKGAVLVH-DAVLTHLVTGRYVMDFHSAD 256

Query: 223 VVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYA 282
           + +  A   +  G   G+I PL  G T+++          +  L   +  ++Y  PT   
Sbjct: 257 IFWCTADPGWVTGSSYGIIAPLLHGITSIIDEADFDAERWYRILEEQRVTVWYTAPTAIR 316

Query: 283 SMLANPDCP-KEGELR-LRACTSAGEAL-PEDVGRRWQAR-FGVDILDGIGSTEMLHIFL 338
            ++     P K  +L  LR   S GE L PE V   W  R  G+ I D    TE   I +
Sbjct: 317 MLMRAAIEPLKRFDLSPLRLIHSVGEPLNPEAVV--WGERVLGLPIHDNWWQTETGGIMI 374

Query: 339 SNRAG-DVHYGTSGKPVPGYR---LRLIDEDGAEITTAGVAGELQI--SGPSSAVMYWNN 392
           +N A  ++  G+ G+P+PG     +R +D+    +T   V G+L +    PS    Y ++
Sbjct: 375 ANYAAMEIRPGSMGRPLPGIEAAIVRRVDDSVDVLTEPDVEGDLALRPGWPSMFRAYLHD 434

Query: 393 PEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVL 452
            E+    F+  W  +GD    + +GYY + GR DD++K SG  V P EVESAL+ H AV 
Sbjct: 435 EERYRKCFVSGWYITGDLAKRDADGYYWFVGRGDDIIKTSGHMVGPFEVESALMEHPAVA 494

Query: 453 EAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLP 512
           EA V+G  +       KAF+ LKPG+   + LR +L    +  L     P+ +EFVD LP
Sbjct: 495 EAGVIGKPEPIIGEIVKAFVCLKPGFEPTDKLRLELIGFGRTRLGSAVAPKEMEFVDSLP 554

Query: 513 KTATGKIQRFKLRS 526
           +T +GKI R  L++
Sbjct: 555 RTRSGKIMRRLLKA 568


Lambda     K      H
   0.319    0.138    0.412 

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: 842
Number of extensions: 50
Number of successful extensions: 4
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: 527
Length of database: 584
Length adjustment: 36
Effective length of query: 491
Effective length of database: 548
Effective search space:   269068
Effective search space used:   269068
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: 53 (25.0 bits)

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

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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