GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum thiophilum BV-S

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_045583514.1 AL072_RS26405 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_001305595.1:WP_045583514.1
          Length = 301

 Score =  349 bits (895), Expect = e-101
 Identities = 169/303 (55%), Positives = 235/303 (77%), Gaps = 5/303 (1%)

Query: 6   HYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGL 65
           +++QQL+NGL++G+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG+++A I    +  +G+
Sbjct: 3   YFIQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGALGI 62

Query: 66  DSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ 125
             VPL +L    AS++ TS +G+++ER+AYRPLR   RL PLISAIGMSIFLQN + + Q
Sbjct: 63  TWVPLALLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYIQILQ 122

Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVV-ISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184
            ++ K +  +LPGN       M+G V +SY+++   V+T ++M G T+ I+R+ LGRA R
Sbjct: 123 GARSKPLQPILPGNLTL----MDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGRAQR 178

Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244
           AC +D KM  LLG+N + +I+LTFV+GAALAAVA +++ + YGVI+  IGFLAG+K+FTA
Sbjct: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKSFTA 238

Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304
           AVLGG+GS+PGAMLGG+++G+ EAF +   G ++KDV  F +L+LVL+FRPTG+LGRPE+
Sbjct: 239 AVLGGVGSLPGAMLGGVVIGLIEAFWSGYVGSEWKDVATFSILVLVLIFRPTGLLGRPEI 298

Query: 305 EKV 307
           EKV
Sbjct: 299 EKV 301


Lambda     K      H
   0.328    0.145    0.413 

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: 367
Number of extensions: 13
Number of successful extensions: 2
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: 307
Length of database: 301
Length adjustment: 27
Effective length of query: 280
Effective length of database: 274
Effective search space:    76720
Effective search space used:    76720
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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