GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Pseudomonas putida KT2440

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 PP_4483 PP_4483 histidine lysine / arginine / ornithine ABC transporter - ATP binding subunit

Query= uniprot:A0A1N7U8S3
         (276 letters)



>FitnessBrowser__Putida:PP_4483
          Length = 254

 Score =  314 bits (805), Expect = 1e-90
 Identities = 166/253 (65%), Positives = 201/253 (79%), Gaps = 3/253 (1%)

Query: 26  KLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITL 85
           KL+V+ +HKRYG HEVLKGVSL A+ GDVIS+IG+SGSGKST LRCIN LEQP AG I L
Sbjct: 3   KLEVQDLHKRYGSHEVLKGVSLAAKAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62

Query: 86  DGISIEMRQGRAGT-RAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144
           +   +++  G+ G  +A    QLQ +R+RL+MVFQHFNLWSHMT LENI  AP  VL V+
Sbjct: 63  NNEELKLVPGKDGALKAADPRQLQRMRSRLSMVFQHFNLWSHMTALENIIEAPVHVLGVN 122

Query: 145 AAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALD 204
             EA ++A  YL KVG+  R  D +P  +SGG+QQRVAIARALAMEPE++LFDEPTSALD
Sbjct: 123 KKEALEKAEHYLAKVGVAHR-KDAFPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALD 181

Query: 205 PELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDAR-ILDQPN 263
           PELVG+VLKV+Q LA+EGRTM++VTHEMGFAR+VS+Q++FLH+G VEE G  R +L  P 
Sbjct: 182 PELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGLVEETGCPREVLANPQ 241

Query: 264 SERLQQFLSNRLK 276
           SERLQQFLS  LK
Sbjct: 242 SERLQQFLSGSLK 254


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: 242
Number of extensions: 6
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: 254
Length adjustment: 25
Effective length of query: 251
Effective length of database: 229
Effective search space:    57479
Effective search space used:    57479
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