GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Rhodobacter maris JA276

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_097070282.1 CRO22_RS11435 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_900217815.1:WP_097070282.1
          Length = 289

 Score =  142 bits (357), Expect = 1e-38
 Identities = 93/297 (31%), Positives = 156/297 (52%), Gaps = 19/297 (6%)

Query: 6   QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65
           Q ++NGL LG+ Y L+A+G T+++ ++ ++NFAHG +++LGGF   I + V+      LP
Sbjct: 3   QIIVNGLFLGASYALIALGLTLIFSLMNVLNFAHGQMYVLGGF---ITYTVVAQFH--LP 57

Query: 66  VAVLLLVMLVVAMLMTSLWNWTIERVAYRPL--RGSFRLAPLITAIGMSITLSNFIQVTQ 123
             V L+   V    + +      ER  + P+  R     + ++ A G++  L     +  
Sbjct: 58  FVVGLICSAVALAALGAF----AERFLFAPVIRRSKREESTMLLAAGIAFFLDAVTLLVF 113

Query: 124 GPRNKPIPPMVSSVYQFG-NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQD 182
           G + + IP +V  V+ +   I +   +I+I  +   L+  F   +  +  GRA RA  QD
Sbjct: 114 GEKQRGIPKIVQGVFNWDFRIVMPYDRILIGCLAVALIAAFILFMRLSRTGRAMRALAQD 173

Query: 183 RKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGG 242
           R  A L+GV+V +   I F +GA LA + G + +   GV +   G    +KAF   ++GG
Sbjct: 174 RMAAELMGVDVGRYSMIGFALGAMLAGLVGGLLVSIVGV-NLGMGGPTSIKAFMMIMIGG 232

Query: 243 IGSLPGAVFGGLLIGLIE----SLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRP 295
            G + GA+ GG ++G++E    SL +AY  I Y  +  F  L   L F+P G++G+P
Sbjct: 233 AGVISGAIAGGFILGMLESVGLSLLAAYGDITY--LVIFVSLLIFLAFRPQGLMGKP 287


Lambda     K      H
   0.329    0.143    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: 304
Number of extensions: 29
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: 300
Length of database: 289
Length adjustment: 26
Effective length of query: 274
Effective length of database: 263
Effective search space:    72062
Effective search space used:    72062
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. 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