GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Lactobacillus silagei IWT126

Align ABC transporter related (characterized, see rationale)
to candidate WP_089136612.1 CES79_RS05995 amino acid ABC transporter ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_002217945.1:WP_089136612.1
          Length = 246

 Score =  207 bits (527), Expect = 2e-58
 Identities = 108/253 (42%), Positives = 170/253 (67%), Gaps = 12/253 (4%)

Query: 5   APVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64
           A   + V+++ K +   H+L  I+    QG+V+++LG SGSGKST +RCLN LE   +G+
Sbjct: 2   AKQVIKVEHLEKYYQKDHILHDINFSIDQGEVVALLGPSGSGKSTLIRCLNGLEPYQNGT 61

Query: 65  VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ 124
           VS  G+++    +   KL           R ++GMVFQ+++L+ ++TVL+N++ GP++VQ
Sbjct: 62  VSFNGDQVVPTEKNWQKL-----------RQKIGMVFQSYDLFPNLTVLDNILLGPVKVQ 110

Query: 125 KRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSA 184
           K+SR  +   AE LL +VGL E    YP  LSGGQ+QR+AI RALA++P++MLFDE T++
Sbjct: 111 KQSRETAKAAAEKLLDQVGLREYENVYPRQLSGGQKQRIAIVRALALNPELMLFDEVTAS 170

Query: 185 LDPELVGEVLRVMRSLAEEG-RTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFV 243
           LDPE+V  VL ++  LA++   TM+VVTHEM FA+ +++RV+FL  G++      D+ F 
Sbjct: 171 LDPEMVRGVLNIISKLAQDSDMTMIVVTHEMNFAQQIADRVLFLEDGKILEQTKGDQFFK 230

Query: 244 ECKSDRFRQFVSS 256
           + ++DR ++F+ S
Sbjct: 231 QPQTDRAKEFLES 243


Lambda     K      H
   0.318    0.133    0.377 

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: 161
Number of extensions: 3
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: 263
Length of database: 246
Length adjustment: 24
Effective length of query: 239
Effective length of database: 222
Effective search space:    53058
Effective search space used:    53058
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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