GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas stutzeri RCH2

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1059 Psest_1092 Branched-chain amino acid ABC-type transport system, permease components

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__psRCH2:GFF1059
          Length = 295

 Score =  136 bits (343), Expect = 5e-37
 Identities = 91/297 (30%), Positives = 146/297 (49%), Gaps = 27/297 (9%)

Query: 7   QLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP- 65
           QLL GL  G+ Y L+++G  +++G++ +INFAHG  +MLG F A          F GL  
Sbjct: 15  QLLLGLINGAFYALLSLGLAIIFGLLRIINFAHGAQYMLGAFVA----------FLGLNY 64

Query: 66  VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGP 125
           + V     LV+A L+       IER   R + G   L  L+   G+++ +        G 
Sbjct: 65  LGVSYWFALVLAPLVVGCLGMAIERGLLRRIAGEDHLYGLLLTFGLALIVEGSFVKLFGV 124

Query: 126 RNK--PIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDR 183
                P+P ++   +  G + +   +  +IV   V+    WY++ RT LG   RA  ++ 
Sbjct: 125 SGSSYPMPELLRGGFNLGFMFLPTYRAWVIVAALVVCLATWYVIERTRLGSYLRAGTENP 184

Query: 184 KMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPG------VKAFTA 237
           K+    G+NV   +++T+  G ALAA AG +    Y V       TPG      +  F  
Sbjct: 185 KLMQGFGINVPLLVTLTYGYGVALAAFAGVLAAPIYAV-------TPGMGSNLLIVVFAV 237

Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
            V+GG+GS+ GA+  G+ +GLIE L   ++  A   V  F ++  VL+ +P G+ G+
Sbjct: 238 VVIGGMGSILGAIVTGIAMGLIEGLTKVFYPEAANTV-VFLVMVAVLLIRPAGLFGK 293


Lambda     K      H
   0.329    0.143    0.421 

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: 322
Number of extensions: 20
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: 300
Length of database: 295
Length adjustment: 26
Effective length of query: 274
Effective length of database: 269
Effective search space:    73706
Effective search space used:    73706
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 (21.8 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