GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Lactobacillus silagei IWT126

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_089136416.1 CES79_RS04320 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_002217945.1:WP_089136416.1
          Length = 314

 Score =  179 bits (455), Expect = 6e-50
 Identities = 98/234 (41%), Positives = 144/234 (61%), Gaps = 4/234 (1%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           ++L NV K +     L  ++LT+ DGE  V VGPSG GK+TLL+ I+ L   T+G++ I 
Sbjct: 2   IELLNVNKEYQEQHALDHLSLTINDGELFVLVGPSGSGKTTLLKTINRLVVPTSGQVKID 61

Query: 64  GQTVTTTP--PAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRML 121
           G+ V        +R I  V Q+ AL+P+++V EN ++ L   + P E+   R+AE    +
Sbjct: 62  GKDVADVDLQQLRRRIGYVLQTGALFPNMTVAENASVQLDNLKWPAEKKHERIAELMTEV 121

Query: 122 SLED--YLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179
            L+   +LDR PSELSGG+ QRV I RA+  +P L L DE  S LD   R   +  +  L
Sbjct: 122 GLDPDHFLDRMPSELSGGEAQRVGIVRALAAKPGLVLMDESFSALDPVSRRQLQQIVINL 181

Query: 180 HRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEF 233
           HR L +++++VTHD  EA+ LAD+I V+ +G+++QVGTP E+   PAN FV+ F
Sbjct: 182 HRDLDSTIVFVTHDMHEALRLADRIAVVYNGKLQQVGTPTEILTEPANAFVSSF 235


Lambda     K      H
   0.320    0.137    0.391 

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: 252
Number of extensions: 9
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: 331
Length of database: 314
Length adjustment: 28
Effective length of query: 303
Effective length of database: 286
Effective search space:    86658
Effective search space used:    86658
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: 48 (23.1 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