GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Acidovorax sp. GW101-3H11

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 Ac3H11_4628 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4628
          Length = 358

 Score =  125 bits (313), Expect = 3e-33
 Identities = 99/339 (29%), Positives = 152/339 (44%), Gaps = 49/339 (14%)

Query: 92  RWAVLALVVVAFVWPFFASRGAVDIATLILIYVM--LGIGLNIVVGLAGLLDLGYVGFYA 149
           R A+  L+ VAFV     +      A LI   +M    +G+N++VG  G + LG   F A
Sbjct: 26  RIAIALLLAVAFVAVPMLASDYFFRAILIPFVIMSLAALGVNVLVGYCGQISLGSGAFMA 85

Query: 150 VGAY-TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLG---FGE 205
           VGAY  Y       G     AL + G+ A  FG L G P LR++G YLA+ TL    F +
Sbjct: 86  VGAYGAYNFFVRLPGLPLIPALILGGLCATFFGILFGLPSLRVKGLYLAVATLAAQFFSD 145

Query: 206 IIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILL 265
            + + +R  T  T  P+G  S+    +FG+  E    +                      
Sbjct: 146 WMFLRIRWFTLDT--PSGSVSVSNLQVFGMPIESATSK---------------------- 181

Query: 266 YVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAG 325
           Y+  L ++++   +   L+R  IGR W A+R+ +VA   +G+ P   KLSAF + +   G
Sbjct: 182 YLFCLAILVVMALMAKNLVRGAIGREWMAIRDMDVAASVIGIRPMYAKLSAFAVSSFIIG 241

Query: 326 FAGSFFA-ARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQ------- 377
            AG  +A    G   P +F+   S  +L +V++GGMGS +G    A  +V+L        
Sbjct: 242 VAGGLWAFVYLGAWEPGAFSVDMSFRLLFMVIIGGMGSIMGSFFGAAFIVVLPIALNQFL 301

Query: 378 -----------EMRGFNEYRMLIFGLTMIVMMIWRPQGL 405
                         G +   ++IFG  ++  +I  P GL
Sbjct: 302 PLFLGLFGISISTAGVSHAELMIFGGLIVWFLIVEPHGL 340


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: 405
Number of extensions: 30
Number of successful extensions: 5
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: 358
Length adjustment: 30
Effective length of query: 387
Effective length of database: 328
Effective search space:   126936
Effective search space used:   126936
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