GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Pseudomonas fluorescens GW456-L13

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PfGW456L13_1967 Arginine/ornithine ABC transporter, ATP-binding protein AotP

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1967
          Length = 254

 Score =  241 bits (615), Expect = 1e-68
 Identities = 121/247 (48%), Positives = 169/247 (68%), Gaps = 11/247 (4%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           +++  ++K YG   VL+ ++L    G+ I I G SGSGKST +RCIN LE+  +G+I+++
Sbjct: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGRILLN 63

Query: 83  GIEL-----------TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131
             EL            +D K + ++RS + MVFQHFNL+ H+T LEN+  AP+ V  V K
Sbjct: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVSK 123

Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191
            EA E A +YL KV +  +   YPG +SGG+QQRVAIAR+L M+P++MLFDEPTSALDPE
Sbjct: 124 AEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183

Query: 192 MIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSE 251
           ++ +VL  M  LA+EG TM+ VTHEMGFA+ V+N+++F+  G + E  NP +   NPQSE
Sbjct: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243

Query: 252 RTKQFLS 258
           R +QFLS
Sbjct: 244 RLQQFLS 250


Lambda     K      H
   0.320    0.134    0.391 

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: 188
Number of extensions: 8
Number of successful extensions: 2
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: 263
Length of database: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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