GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Phaeacidiphilus oryzae TH49

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  224 bits (570), Expect = 4e-63
 Identities = 132/290 (45%), Positives = 172/290 (59%), Gaps = 8/290 (2%)

Query: 3   DIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLR 62
           D+    L K + G    +  +DL I  G F  LLG SGCGK+T LRMI+GLE  + G + 
Sbjct: 18  DLRLTGLTKKF-GSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIH 76

Query: 63  IGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALL 122
           +G   V D     R V  VFQNYAL+PH+ +++N+AFGLRR  R    + + V ++  L+
Sbjct: 77  LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRR--RGIRSVKKPVEDMLDLV 134

Query: 123 NLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQ 182
            L  L  RKP  +SGGQQQR A+ARA+I  P V L DEPL  LD KLR Q++ ++KR+  
Sbjct: 135 ELGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQL 194

Query: 183 RLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNF 242
            +  T V+VTHDQ EAMT+AD + +M  GRI Q GSPAELY  P   F A F+G    N 
Sbjct: 195 EVGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNL 252

Query: 243 LSGTVQRQDGQLFIETAHQR-WALTGERFSRLRHAMAVKLAVRPDHVRIA 291
           ++GTV+   G +    AH R  AL   R      +  V L VRP+ VRIA
Sbjct: 253 IAGTVESVSGDVVQVAAHGRSLALPAARCRTT--SGPVILGVRPEKVRIA 300


Lambda     K      H
   0.321    0.137    0.403 

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: 364
Number of extensions: 15
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: 406
Length of database: 386
Length adjustment: 31
Effective length of query: 375
Effective length of database: 355
Effective search space:   133125
Effective search space used:   133125
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: 50 (23.9 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