Alignments for a candidate for hcl in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcl in Cupriavidus basilensis 4G11

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate RR42_RS35150 RR42_RS35150 4-hydroxybenzoate--CoA ligase

Query= SwissProt::Q8GQN9
         (527 letters)



>FitnessBrowser__Cup4G11:RR42_RS35150
          Length = 523

 Score =  525 bits (1352), Expect = e-153
 Identities = 286/510 (56%), Positives = 345/510 (67%), Gaps = 13/510 (2%)

Query: 22  YNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVC 81
           +N A  LI  N  A R GKT YIDD G+ +Y ELA R+ R  +AL+ + G+  ++RVL+ 
Sbjct: 14  FNFAQHLIACN--ARRPGKTAYIDDHGAMSYGELAERIRRVAAALQAS-GIHREERVLLL 70

Query: 82  VLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLG 141
           + DG D+P  FLGA+  G+VP+A+NTLLT  DY YML  S A+  +VS  LLP+    + 
Sbjct: 71  MHDGNDWPVCFLGAMYAGIVPVAVNTLLTADDYAYMLQHSRAQAVLVSGALLPVLQQAMA 130

Query: 142 KVPTLEHLVVAG---GAGEDSLAAL---LATGSEQFEAAPTRPDDHCFWLYSSGSTGAPK 195
           +       V+     G   D + AL   +   +     A T PDD  FWLYSSGSTG PK
Sbjct: 131 QGGHEAGTVIVSQPAGPLPDGMIALDGWIDRTAPLAAPASTSPDDPGFWLYSSGSTGRPK 190

Query: 196 GTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAE 255
           G +H   +   TAELYA+P+L + E D+ FSAAKL+FAYGLGN L FPL+VGAT VLMAE
Sbjct: 191 GVLHSQGNPYWTAELYAKPVLSLGEADICFSAAKLYFAYGLGNALTFPLSVGATVVLMAE 250

Query: 256 RPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRR 315
           RPTP A F R   +QP +F+G PT YA MLA P  P   ++ LR C+SAGEALP D+G R
Sbjct: 251 RPTPEATFRRWLDYQPTVFFGAPTGYAGMLAAPGLPTREQVSLRLCSSAGEALPADLGER 310

Query: 316 WQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVA 375
           + A FG +I+DGIGSTEMLHIFLSNR G V YGT+G PVPGY + L DEDG  +   G  
Sbjct: 311 FTAHFGCEIIDGIGSTEMLHIFLSNRPGQVRYGTTGWPVPGYAVELRDEDGHAVPD-GDV 369

Query: 376 GELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIY 435
           G+L I GPS+A+MYW N EK+  TF G WT+SGDKY  N +G Y YAGRSDDMLKVSGIY
Sbjct: 370 GDLYIQGPSAALMYWGNREKSRETFRGGWTKSGDKYARNADGSYSYAGRSDDMLKVSGIY 429

Query: 436 VSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNL 495
           VSP EVE+ L  H AVLEAAV+G  D   L K KAF+VLKPG    E   T+LKA VK  
Sbjct: 430 VSPFEVEATLAQHPAVLEAAVIGVPDPAGLTKTKAFVVLKPGAQVSE---TELKAFVKER 486

Query: 496 LAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
           LAPYKYPR IEF+  LPKTATGKIQRF+LR
Sbjct: 487 LAPYKYPRVIEFMGALPKTATGKIQRFRLR 516


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: 862
Number of extensions: 34
Number of successful extensions: 5
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: 523
Length adjustment: 35
Effective length of query: 492
Effective length of database: 488
Effective search space:   240096
Effective search space used:   240096
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: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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