GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudomonas simiae WCS417

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3280 PS417_16790 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__WCS417:GFF3280
          Length = 293

 Score =  123 bits (309), Expect = 4e-33
 Identities = 91/305 (29%), Positives = 154/305 (50%), Gaps = 17/305 (5%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M +F + LL GL  G++Y LVAIG+ ++Y   G+ NFA G + +   FAAL  F+ L   
Sbjct: 1   MTFFFETLLGGLLAGTMYSLVAIGFVLIYKASGVFNFAQGSMLL---FAAL-TFVSLHD- 55

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
             G+P A+ LLV ++V ++   L    IER+  RPL    ++   +  +G+S  +    Q
Sbjct: 56  -QGVPFALALLVTVIVMIVGALL----IERLVLRPLVNRSQITLFMATLGLSFIIEGLAQ 110

Query: 121 VTQGPRNKPIPPMVSSVYQF-GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
              G + + +   +  V  F G + +S   +I      VL+T+   + N+T +G + RA 
Sbjct: 111 GLMGSQVRALDLGIDDVPLFVGPLMLSQFDLIAAAAAVVLVTVLALLFNKTRIGVSLRAV 170

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
             D   A  +G+N+++   I + +   +  VAG ++    GV  F+      +KA    +
Sbjct: 171 ADDTTAALSIGINLNRIWQIVWAVAGIVGLVAGLLWGARQGV-QFSLSLVV-LKALPVLI 228

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYF--TIAYKDVATFA-ILAFVLIF-KPTGILGRP 295
           +GG  S+ GA+ GGL++G  E+L   Y    I       FA +LA   ++ +P G+ G  
Sbjct: 229 IGGFTSIGGAIVGGLIVGAAENLAEVYIGPLIGGGITPWFAYVLALAFLYIRPAGLFGER 288

Query: 296 EVEKV 300
            +E+V
Sbjct: 289 AIERV 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: 293
Number of extensions: 20
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: 300
Length of database: 293
Length adjustment: 26
Effective length of query: 274
Effective length of database: 267
Effective search space:    73158
Effective search space used:    73158
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