GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_04061 H281DRAFT_04061 amino acid/amide ABC transporter membrane protein 2, HAAT family

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Burk376:H281DRAFT_04061
          Length = 389

 Score =  244 bits (622), Expect = 4e-69
 Identities = 149/330 (45%), Positives = 191/330 (57%), Gaps = 47/330 (14%)

Query: 114 VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALL------------AEY 161
           V +    ++YVML +GLN+VVG AGLLDLGY+ FYAVGAYT ALL            A  
Sbjct: 49  VRVLDFAMLYVMLALGLNVVVGFAGLLDLGYIAFYAVGAYTAALLSSPHLTSQFEWIAHL 108

Query: 162 AGFG----FWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNM--- 214
           A  G    F   +P A  +AA FG +LG P LRLRGDYLAIVTLGFGEI+RI L N+   
Sbjct: 109 APNGLHVPFLIIVPCAMAVAAFFGVILGAPTLRLRGDYLAIVTLGFGEIVRIFLNNLDRP 168

Query: 215 TEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVL 274
             IT GP GI  I    L   +  +         H  FG  + + Y    L+V+A LLV+
Sbjct: 169 VNITNGPKGITGIDSVHLGDFSLAQT--------HSLFGFQFPSVYSYYYLFVLAALLVI 220

Query: 275 LALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAAR 334
              +V  RL    IGRAW A+REDE+A +A+G+N   VKL AF +GASF G +G+ F A 
Sbjct: 221 ---WVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMFGAF 277

Query: 335 QGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL-----------------Q 377
           QG V+PESFT  ES ++LA VVLGGMG   GVIL AV++ +L                  
Sbjct: 278 QGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLLAVLPEFLRSTMGPLQHMLFGH 337

Query: 378 EMRGFNEYRMLIFGLTMIVMMIWRPQGLLP 407
           E+      R L++ L M+++M++R +GL P
Sbjct: 338 EIVDTEVIRQLVYALAMVLIMLYRSEGLWP 367


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: 459
Number of extensions: 26
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: 389
Length adjustment: 31
Effective length of query: 386
Effective length of database: 358
Effective search space:   138188
Effective search space used:   138188
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 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