GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas stutzeri RCH2

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__psRCH2:GFF4209
          Length = 383

 Score =  108 bits (270), Expect = 2e-28
 Identities = 75/236 (31%), Positives = 129/236 (54%), Gaps = 16/236 (6%)

Query: 3   QEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62
           ++ +L    + K++    A+D     ++ GEI A++G +G+GKS++++ ++G   P EG 
Sbjct: 19  KQVLLKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGR 78

Query: 63  IRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122
           I L+G+ I    P E     I  ++Q+ AL P +++  N+  G  +++ G        L 
Sbjct: 79  IFLDGQDITDMPPYE---RPINMMFQSYALFPHMTVEQNIAFG--LKQDG--------LP 125

Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182
           +A +E++ +  L  L  MT Q   +    LSGGQRQ VA+AR+ A   K++++DEP  AL
Sbjct: 126 KAEIEERVKEMLG-LVQMT-QYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 183

Query: 183 GVK-ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKD 237
             K  S+  LEL+  + R G+  V+++H+      +A+RI I  LG    V +P D
Sbjct: 184 DKKLRSQMQLELVQIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMD 239


Lambda     K      H
   0.321    0.136    0.383 

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: 164
Number of extensions: 3
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: 260
Length of database: 383
Length adjustment: 27
Effective length of query: 233
Effective length of database: 356
Effective search space:    82948
Effective search space used:    82948
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: 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