GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Amycolatopsis halophila YIM 93223

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_034278233.1 AMYHA_RS20915 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000504245.1:WP_034278233.1
          Length = 366

 Score =  144 bits (362), Expect = 6e-39
 Identities = 108/339 (31%), Positives = 168/339 (49%), Gaps = 43/339 (12%)

Query: 94  AVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAY 153
           AV A+V++A   P+      + +  L     +  IGLNIV G AG + LG+  F A+GAY
Sbjct: 26  AVGAIVLLALAMPWLVQDRTLSLLALACAASIGAIGLNIVTGYAGQVSLGHAFFLAIGAY 85

Query: 154 TYALLA-----EYAGFGFWTALP---IAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGE 205
           T A L+        GFG    L     AG++AA+FG L+     RLRG YLAIVTLG   
Sbjct: 86  TAAALSGDPDGRTIGFGVTNVLVWLLAAGLVAAVFGVLVAPLATRLRGLYLAIVTLGLVF 145

Query: 206 IIRILLRNMTEITGGPNGIGSI-PKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVIL 264
           I   + +   ++TGG  G+G   P P LFG+T  +             G    ++ K+ L
Sbjct: 146 IGEHVFKEWRDLTGGA-GVGRPGPVPELFGVTLNKS------------GDVLTSDQKLYL 192

Query: 265 LYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFA 324
           L +V L  V+L +   N L R  +GRA+ A+R+ ++A   +G+N    K+ AF + + +A
Sbjct: 193 LMLVCL--VVLGILARN-LARSKVGRAFAAIRDRDIAASVIGVNLARYKMIAFAVSSFYA 249

Query: 325 GFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMR---- 380
           G AG+      G + P SF  + S   +A+V++GG+ +  G I+ A  + LL  +     
Sbjct: 250 GCAGALLYTITGFIEPTSFNLLLSVQYIAMVLIGGVATISGSIMGAFFITLLPALTRELP 309

Query: 381 --------------GFNEYRMLIFGLTMIVMMIWRPQGL 405
                            +   +++GL +I  +I+ P+GL
Sbjct: 310 TVAPFISSDASAPLNVFQVETVLYGLLIIGFLIFEPRGL 348


Lambda     K      H
   0.330    0.146    0.439 

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: 446
Number of extensions: 29
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: 417
Length of database: 366
Length adjustment: 31
Effective length of query: 386
Effective length of database: 335
Effective search space:   129310
Effective search space used:   129310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 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