GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Methanococcus aeolicus Nankai-3

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_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  130 bits (327), Expect = 3e-35
 Identities = 86/233 (36%), Positives = 134/233 (57%), Gaps = 18/233 (7%)

Query: 27  LQVEGIHKRYGEHE----VLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGV 82
           ++ + I K YG  E    VL+G++L  ++G+ ++++G SG GKST+L  +  L+ P+ G+
Sbjct: 18  IEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGM 77

Query: 83  ITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLD 142
           + +        +G+  T     D+    R     +FQ FNL + +T LEN+ +    VLD
Sbjct: 78  VYI--------KGKKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVELP--LVLD 127

Query: 143 VSAAEAE-KRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTS 201
                   K+A+  L  + L  R  + YP  LSGGQQQRVAIARAL+  P+II  DEPT 
Sbjct: 128 EKNKNYRIKKAKKLLKIINLGHR-ENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTG 186

Query: 202 ALDPELVGEVLKVIQTLAE-EGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEH 253
            LD +   EV+ +++ L E EG T++MVTHE  FA+  +S+++ +  G + EH
Sbjct: 187 NLDSKNSREVMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVEH 238


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: 153
Number of extensions: 10
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: 238
Length adjustment: 24
Effective length of query: 252
Effective length of database: 214
Effective search space:    53928
Effective search space used:    53928
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 Apr 09 2024. 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