GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

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



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  192 bits (487), Expect = 1e-53
 Identities = 108/235 (45%), Positives = 146/235 (62%), Gaps = 12/235 (5%)

Query: 12  NFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEE 71
           N  A   +D+LNL+I  GE + LLG SGCGK+T L  +AG    + G+I I D  V  + 
Sbjct: 14  NRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIRIGDEVVYDDR 73

Query: 72  ----PKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLL 127
               P+ RGIGMVFQ YAL+P +T+EKN++FGL   K        + KRA E+L++  L 
Sbjct: 74  RALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN-----RDKKKRAQEVLELVGLG 128

Query: 128 K---RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLK 184
           +   R PSELSGGQ+QRVA+ RAL     V L DEP SNLDA LR ++R ++  + +   
Sbjct: 129 EFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRYDVTNILRKAN 188

Query: 185 NTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239
            T I VTHDQ +A  ++DR+ VM  G+IQQ+A P  +Y  P N FVA F+G  ++
Sbjct: 189 ATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKTNL 243


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: 308
Number of extensions: 14
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: 361
Length of database: 351
Length adjustment: 29
Effective length of query: 332
Effective length of database: 322
Effective search space:   106904
Effective search space used:   106904
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