GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas simiae WCS417

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF3451 PS417_17665 ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__WCS417:GFF3451
          Length = 286

 Score =  160 bits (404), Expect = 4e-44
 Identities = 98/298 (32%), Positives = 166/298 (55%), Gaps = 20/298 (6%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           YL Q++NGL +G  Y LI++G T+++G++  +NFAHG  +++G+YI + A++L     L 
Sbjct: 5   YLFQILNGLGLGMIYFLISVGLTIIFGLLNFVNFAHGAFFLLGAYICYTAVSLTGNFWL- 63

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVML--S 124
                   A   + +V +A  + IERV  + +     +  ++  +G+++ +Q A ++   
Sbjct: 64  --------ALLIAPLVVAALAWVIERVLIQRIYHLPHMFQILVTLGIALIIQEASVMIWG 115

Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184
              K  A+P LL G  V G+      V  Y ++ + V + LV  GL L + R+R G   R
Sbjct: 116 PVGKSVAVPELLRGVLVVGD-----FVYPYYRLFLIVFSGLVGLGLWLLLERTRFGALVR 170

Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIG-FLAGIKAFT 243
           A +E  +  +LLG N   + ++TF +G ALA VA VL     G   P +G  + G+ AF 
Sbjct: 171 AGSESTETVSLLGTNIFRLFSMTFALGVALAGVAGVLFAPLRGA-QPFVGPEILGV-AFV 228

Query: 244 AAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301
             V+GG+GS  GA++GGLL+GV ++    ++  Q   ++ +G + +V+L RP G+ GR
Sbjct: 229 VVVIGGMGSFSGALVGGLLVGVVQSLMTTLW-PQGASLMIYGAMAVVILVRPYGLFGR 285


Lambda     K      H
   0.328    0.145    0.413 

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: 258
Number of extensions: 13
Number of successful extensions: 4
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: 307
Length of database: 286
Length adjustment: 26
Effective length of query: 281
Effective length of database: 260
Effective search space:    73060
Effective search space used:    73060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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