GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Nocardiopsis baichengensis YIM 90130

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_017557175.1 C892_RS0110670 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000341205.1:WP_017557175.1
          Length = 370

 Score =  102 bits (255), Expect = 1e-26
 Identities = 97/334 (29%), Positives = 152/334 (45%), Gaps = 50/334 (14%)

Query: 93  WAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGA 152
           WAV AL  VA +         + +A + L +++   GL  +VG +G + LG+  F  VG+
Sbjct: 45  WAVAALAAVAALTAATGPVTDLRVANVGL-HLLAVAGLQFLVGTSGQVSLGHGAFMFVGS 103

Query: 153 YTYALLAEYAGFGFWTALPIAGMMAA------LFGFLLGFPVLRLRGDYLAIVTLGFGEI 206
           Y  ALL          A+P+A  MAA      L G ++G    RL G YLA  TL     
Sbjct: 104 YAMALLVVNV-----PAMPLAAGMAAACAAGCLAGLVVGAATARLHGPYLAGATLMLAVG 158

Query: 207 IRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLY 266
           +  +     ++ GG NG+                A  G   F    G   +T ++ I+++
Sbjct: 159 LPAIALRFPDLLGGANGLAF--------------ATIGAPPF--LAGAVDDTQWRAIVVW 202

Query: 267 VVALL-LVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAG 325
            VAL+ LV+LA     RL     GR   ALR+D  A    G+     +++AF I A    
Sbjct: 203 TVALIGLVVLATASAGRL-----GRHLRALRDDAAAASLSGVPVGRARVTAFVISAGAGS 257

Query: 326 FAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQ-------- 377
            AG+  A   G  TP ++    S ++LA +VLGG+GS  G   AA+ +V ++        
Sbjct: 258 LAGACQAYVLGTATPSTYGLSLSLVLLAALVLGGLGSLWGAFWAALAIVYVEAAGTELAH 317

Query: 378 ------EMRGFNEYRMLIFGLTMIVMMIWRPQGL 405
                 ++R  N   ++ FG  +I +++  P+G+
Sbjct: 318 ALDLSTDVR--NNLPVVFFGAVLITVVLAWPRGV 349


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: 395
Number of extensions: 25
Number of successful extensions: 3
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: 370
Length adjustment: 31
Effective length of query: 386
Effective length of database: 339
Effective search space:   130854
Effective search space used:   130854
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