GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Geotalea uraniireducens Rf4

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  205 bits (522), Expect = 1e-57
 Identities = 127/298 (42%), Positives = 180/298 (60%), Gaps = 12/298 (4%)

Query: 1   MTSV--SVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58
           MTS+  SV DL +  G   +L  ++LD++ GE + LLG SG GK+TLL  IAGL   S G
Sbjct: 1   MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60

Query: 59  QIFIKDRNVTWEEPK------DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEK 112
            I I ++ V     K       R +G VFQSYAL+P  TV +N+++GLK+ K+P  EI +
Sbjct: 61  SIRIGEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQ 120

Query: 113 RVKRASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSEL 172
           RV+     L +  L +R P +LSGGQ+QRVA+ R+LV +  V L DEPLSNLDAKLR E 
Sbjct: 121 RVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEA 180

Query: 173 RVEIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAG 232
           R+ +++L   L  + + VTHDQ EA+ +AD++ ++K GVI+Q   P  +Y AP++LFVA 
Sbjct: 181 RIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAE 240

Query: 233 FIGSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV 290
           F+G  + N   G V   DG S  R  G  + +      T L+ G +    +R E +K+
Sbjct: 241 FMG--ANNTISGLVTDVDGDS-ARIEGNGWALRG-RLRTPLKAGDRATAVVRLEKIKL 294


Lambda     K      H
   0.320    0.137    0.392 

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: 321
Number of extensions: 12
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: 361
Length of database: 353
Length adjustment: 29
Effective length of query: 332
Effective length of database: 324
Effective search space:   107568
Effective search space used:   107568
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: 49 (23.5 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