GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO353_11720 AO353_11720 taurine transporter ATP-binding subunit

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11720
          Length = 264

 Score =  192 bits (487), Expect = 8e-54
 Identities = 101/258 (39%), Positives = 148/258 (57%), Gaps = 5/258 (1%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           +++  + R+     G     L  +   +     +  LGPSG GK++LL ++AG    ++G
Sbjct: 1   MALLQLERISAQYPGTAEPVLADISLSLGPQQLLVALGPSGSGKTSLLNLIAGFVEPSAG 60

Query: 64  RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKV 123
           R+ LDG PV+GP AERG+VFQ   L PW  +  N+ FGL   G+P  +++ RA   +A V
Sbjct: 61  RITLDGVPVKGPSAERGVVFQDDALLPWQDVLANVGFGLELAGVPRDKREVRAREMLALV 120

Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183
            L GF+     QLSGG +QR  +ARALA DP++LLMDEPFGALD  TR  MQELLL +W 
Sbjct: 121 DLAGFDARRIWQLSGGQKQRVGLARALAADPRVLLMDEPFGALDAFTREQMQELLLQVWR 180

Query: 184 AERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPH-----PRHYTIKTSPEF 238
              K V  +THDI+EA+F+A  + + +  PG+I   L +D             IK+ P F
Sbjct: 181 RTAKPVFLITHDIEEAVFLATDLILLAPNPGQIVERLLLDFGQRYAAGESARAIKSDPRF 240

Query: 239 MDLKARLTEEIRAESMAA 256
           ++ +  +   + ++  AA
Sbjct: 241 IETREHVLARVFSQRNAA 258


Lambda     K      H
   0.322    0.136    0.394 

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: 204
Number of extensions: 8
Number of successful extensions: 1
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: 259
Length of database: 264
Length adjustment: 25
Effective length of query: 234
Effective length of database: 239
Effective search space:    55926
Effective search space used:    55926
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 (21.9 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