GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Hippea jasoniae Mar08-272r

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 WP_035586711.1 EK17_RS00965 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_000744435.1:WP_035586711.1
          Length = 223

 Score =  126 bits (317), Expect = 4e-34
 Identities = 81/233 (34%), Positives = 134/233 (57%), Gaps = 22/233 (9%)

Query: 27  LQVEGIHKRY--GEH--EVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGV 82
           ++ +GI+K +  G+   EVLK ++L  ++  +++L+G SGSGKST+L  +  L  PD+G 
Sbjct: 4   IEAKGIYKSFKSGQETIEVLKSINLEIKKSQMVALMGVSGSGKSTLLHILGLLSAPDSGE 63

Query: 83  ITLDGISIEMRQGRAGTRAPHQDQLQNLRTR-LAMVFQHFNLWSHMTVLENITMAPRRVL 141
           +   G  I+            ++ L   R + +  VFQ ++L   +T+LENI M P  + 
Sbjct: 64  VIFSGSKIDFTS---------EENLALFRNKHIGFVFQFYSLLGELTILENI-MLPSLI- 112

Query: 142 DVSAAEAEK-RARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPT 200
              A +++K +A   L+ VG P   A+ YP+ LSGGQ QR+A+ARAL   P+I++ DEPT
Sbjct: 113 ---AKKSDKTKALELLNLVGFPQNRANNYPSMLSGGQLQRIALARALINSPDIVIADEPT 169

Query: 201 SALDPELVGEVLKVIQTL-AEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEE 252
           + LD     +++K ++++  E G+T L+ TH    A     +VL +  G+V E
Sbjct: 170 ANLDKNSSIDIVKAMRSINKENGQTFLIATHSSEVA-DYCDKVLVISGGQVSE 221


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: 132
Number of extensions: 6
Number of successful extensions: 3
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: 223
Length adjustment: 24
Effective length of query: 252
Effective length of database: 199
Effective search space:    50148
Effective search space used:    50148
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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