GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Azospirillum brasilense Sp245

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 AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__azobra:AZOBR_RS25635
          Length = 328

 Score =  201 bits (512), Expect = 2e-56
 Identities = 115/314 (36%), Positives = 174/314 (55%), Gaps = 23/314 (7%)

Query: 94  AVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAY 153
           A+L  V +  V   F       IA L LI+++L   +++V G+AGLL LG+  FY VGAY
Sbjct: 8   ALLVFVGLPAVLAGFDRGYFYQIANLALIFILLSASMHLVTGVAGLLHLGHAAFYGVGAY 67

Query: 154 TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRN 213
           T ALL+   G GF   LP++G++AAL  FL+  P +RL   Y A+ TL  G+++ +++ N
Sbjct: 68  TAALLSTKFGLGFTVTLPLSGLVAALIAFLVALPTMRLVSIYFAVATLAIGQMLYLVMLN 127

Query: 214 MTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLV 273
             E T GPNGI       LFG +   R                      +  Y     +V
Sbjct: 128 WVEFTKGPNGIIVTKGLELFGFSLSGR----------------------LATYYTVATVV 165

Query: 274 LLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAA 333
            L +  I RL     G A  ++RED+    A+G++   +K+ AFT+ A FAG AGS +A 
Sbjct: 166 ALCVLAIGRLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFAGVAGSLWAH 225

Query: 334 RQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGL 392
             G ++P  F F ES +ILA+VV+GG+GS  G ++ A++++LL E +R F ++R ++ GL
Sbjct: 226 MTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLRAFGDFRNIMVGL 285

Query: 393 TMIVMMIWRPQGLL 406
            M + ++  P+GLL
Sbjct: 286 VMFLSILLLPKGLL 299


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: 387
Number of extensions: 29
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: 328
Length adjustment: 30
Effective length of query: 387
Effective length of database: 298
Effective search space:   115326
Effective search space used:   115326
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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