GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Dechlorosoma suillum PS

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 Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__PS:Dsui_2059
          Length = 287

 Score =  159 bits (402), Expect = 1e-43
 Identities = 100/290 (34%), Positives = 158/290 (54%), Gaps = 36/290 (12%)

Query: 122 IYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFG 181
           ++ +L + + + +   GLL L    F  VGAY  ALL  +  + F + L   G+   L  
Sbjct: 20  VHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTLHLEWSFGSVLLAGGIAPTLVA 78

Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRA 241
            ++G PVLRL G YLA+ TL FGE++RI + N+ EITGGP G+  IP  T          
Sbjct: 79  LIIGAPVLRLSGVYLAMATLAFGEVVRITVLNL-EITGGPEGLNGIPLAT---------- 127

Query: 242 PEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVA 301
            EG                     + +AL+L  +A++ + RL R  +GRA+EA++EDEVA
Sbjct: 128 -EG---------------------WHIALILA-VAVYGLARLRRSKVGRAFEAIKEDEVA 164

Query: 302 CRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMG 361
            R +G+N    KL AF++GA  AG AG+  A     ++P  + F  +  IL + VLGG  
Sbjct: 165 ARLMGINVDRYKLLAFSLGAFIAGVAGALNAHFTFFISPREYGFENAVDILTMAVLGGTS 224

Query: 362 SQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410
           S +G +L + ++ LL E +R   ++R L+ G  +++++++ P+GL   +R
Sbjct: 225 SLIGPMLGSSILTLLPELLRSLQDFRSLVNGAVLVLVVLFLPKGLWESRR 274


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: 302
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 287
Length adjustment: 29
Effective length of query: 388
Effective length of database: 258
Effective search space:   100104
Effective search space used:   100104
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.

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