GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align tartronate semialdehyde reductase 2 (characterized)
to candidate WP_279338484.1 HTA01S_RS01495 NAD(P)-dependent oxidoreductase

Query= ecocyc::G6278-MONOMER
         (292 letters)



>NCBI__GCF_001592305.1:WP_279338484.1
          Length = 301

 Score =  214 bits (546), Expect = 1e-60
 Identities = 124/291 (42%), Positives = 180/291 (61%), Gaps = 5/291 (1%)

Query: 3   LGFIGLGIMGTPMAINLARAGHQLHVTTIGP-VADELLSLGAVSVETARQVTEASDIIFI 61
           +  +G+G+MG P+A  L  AG+Q+      P  A+ L   GA   +T  Q    +D++  
Sbjct: 15  IAVLGIGMMGWPIARRLCVAGYQVSAWNRSPDKAERLRPFGAQVCDTPAQAVAQADLVIT 74

Query: 62  MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121
           ++ D   VE+VLF + G T+    G  +VDMSSI P + +  A ++  +G  +LDAPVSG
Sbjct: 75  LLEDGKVVEDVLFRQ-GTTEGLRPGALVVDMSSIQPRQARDHAARLAAIGVHHLDAPVSG 133

Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181
           G +GA + TL+IM GG  A FER +P+FE LG+  T VG +G GQ  K+ANQ+IV + I 
Sbjct: 134 GTVGAEQATLAIMAGGKPADFERARPVFEHLGRP-THVGPHGSGQLAKLANQMIVGITIG 192

Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241
           AV+EALL   K GAD  +VRQA+ GGFA SRIL+VHG+RM++R F     I++  KD+  
Sbjct: 193 AVAEALLLCEKGGADMAKVRQAITGGFADSRILQVHGQRMVERDFAKRGAISVQLKDMRN 252

Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           A+ +A+ +    P TA  ++LF   A +G + LDHSAL   +EL + + +A
Sbjct: 253 AMATAREIGFEAPITALFEQLFAQAADHGLADLDHSALF--VELASRNGMA 301


Lambda     K      H
   0.318    0.135    0.376 

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: 237
Number of extensions: 7
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: 292
Length of database: 301
Length adjustment: 26
Effective length of query: 266
Effective length of database: 275
Effective search space:    73150
Effective search space used:    73150
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: 48 (23.1 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:

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:

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:

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:

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