GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Shewanella loihica PV-4

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 5210878 Shew_3304 ABC transporter-related protein (RefSeq)

Query= uniprot:A0A1N7U8S3
         (276 letters)



>FitnessBrowser__PV4:5210878
          Length = 292

 Score =  133 bits (335), Expect = 4e-36
 Identities = 83/261 (31%), Positives = 146/261 (55%), Gaps = 13/261 (4%)

Query: 12  PVDEPVAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRC 71
           P+++   + V   +++   G  +  G H +   VSL   +G V +++G SG GK+T+L+ 
Sbjct: 18  PMEQAPMEHVQPLVEISHLGFSR--GTHVIYDDVSLTIPRGKVTAIMGPSGIGKTTLLKL 75

Query: 72  INFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLE 131
           I    +PD+GVI +DG+ +            ++ +L  LR R++M+FQ   L++ M V +
Sbjct: 76  IGGQLRPDSGVIKVDGVDVHKC---------NRSELFALRKRMSMLFQSGALFTDMNVFD 126

Query: 132 NITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEP 191
           N+  A R   D+  A   +   M L+ VGL    A   P+ LSGG Q+R A+ARA+A+EP
Sbjct: 127 NVAFALREHSDLPEAIIRRIVLMKLEAVGLRG-AAQMMPSELSGGMQRRAALARAIALEP 185

Query: 192 EIILFDEPTSALDPELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRV 250
           E++L+DEP +  DP  +G ++K+I+ L++    T ++V+H++     ++  V  L   +V
Sbjct: 186 ELVLYDEPFAGQDPISMGVLVKLIRELSDALSLTSVVVSHDVQEVLGIADYVYVLADKKV 245

Query: 251 EEHGDARILDQPNSERLQQFL 271
             HG    L   ++ +L+QF+
Sbjct: 246 IAHGTPAELKAADNPKLKQFI 266


Lambda     K      H
   0.319    0.133    0.372 

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: 171
Number of extensions: 9
Number of successful extensions: 4
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: 276
Length of database: 292
Length adjustment: 26
Effective length of query: 250
Effective length of database: 266
Effective search space:    66500
Effective search space used:    66500
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