GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Desulfacinum infernum DSM 9756

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

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



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  278 bits (712), Expect = 1e-79
 Identities = 157/343 (45%), Positives = 213/343 (62%), Gaps = 20/343 (5%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           +++ +V K +G V+ ++ ++ +VE+G+ +V +GPSGCGK+TLLR+I+GLE  T+G I I 
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 64  GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123
           G  VT  PP KR I+MVFQSYAL+PHL+VREN+   LK  + P +EI  R+     +L L
Sbjct: 63  GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122

Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183
              LD +P ELSGG +QRVA+GRA++ E  + L DEPLSNLDA LR + R EI  L R+L
Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182

Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVP 243
             +MIYVTHDQ+EAMT+AD+IV++RDG+I Q  +P   Y  PAN FVA FIG P MN VP
Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242

Query: 244 --------AQRLGGN---PGQ-----FIGIRPEYARISPVGPLAGEVIHVEKLGGDTNIL 287
                   A   GG    PG        GIRPE  R++  G  A  V   E LG DT + 
Sbjct: 243 LCPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLAESGQPA-MVTGREYLGSDTFVS 301

Query: 288 VDM-GEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQ 329
            ++ G+++    R  G+ +   G  +   +DP +   FD   Q
Sbjct: 302 CEIHGQEVIVRTR--GRRNIREGTVVHLTWDPGDVNLFDARTQ 342


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: 339
Number of extensions: 12
Number of successful extensions: 1
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: 365
Length adjustment: 29
Effective length of query: 302
Effective length of database: 336
Effective search space:   101472
Effective search space used:   101472
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