GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Sinorhizobium meliloti 1021

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc02359 SMc02359 high-affinity branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Smeli:SMc02359
          Length = 296

 Score =  160 bits (405), Expect = 3e-44
 Identities = 98/300 (32%), Positives = 164/300 (54%), Gaps = 15/300 (5%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M + +Q +++ L+LG  Y L+A+G  ++YGI+ ++NFA+G++ M+ G+    +FL   S 
Sbjct: 1   MAFAIQFVIDVLSLGGAYALMALGLVIIYGILRLVNFAYGELIMVAGYT---MFLASGS- 56

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSN--F 118
             GLP     +VM V+A+ M  L+    +  A+RP+R     A LIT+   S  L N   
Sbjct: 57  --GLP----WIVMAVLAVGMAILFGIITDYAAFRPVRAKSVTAVLITSFAFSNLLQNAAL 110

Query: 119 IQVTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
           + ++  PRN P+P + S     G     ++ +I I  +  LL    +++ RT LG A RA
Sbjct: 111 LFISPRPRNVPLPDIFSQTVSIGGAITPVRNLITIAASIALLAGVAFLMRRTTLGIAMRA 170

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
              +  MA +LGV  +  IS  F +   LA V G +++   G      G  P + AF A 
Sbjct: 171 AATNFTMARMLGVPANLIISSAFALSGFLAGVVGILWIGRIGTVVPGIGLEPLLVAFIAT 230

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFT---IAYKDVATFAILAFVLIFKPTGILGRP 295
           V+GG+ SLPGAV GG L+ LI++  +   +   + ++D  TF+++  +L+++P G++  P
Sbjct: 231 VIGGMRSLPGAVVGGFLLALIDTTLNYTLSQDLLKFRDAFTFSLVILILLWRPDGLIRGP 290


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: 287
Number of extensions: 26
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: 296
Length adjustment: 26
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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