GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Malonomonas rubra DSM 5091

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  157 bits (396), Expect = 6e-43
 Identities = 88/243 (36%), Positives = 141/243 (58%), Gaps = 8/243 (3%)

Query: 15  TTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTT----- 69
           TT  + D + +I  GE  V +G SG GKST++R L  L   +SG++ I G D+       
Sbjct: 42  TTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQ 101

Query: 70  -VEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLD 128
            V+     L+MVFQS+AL PHMTV +N  FG++++G +   R++R  +A   + LE + +
Sbjct: 102 LVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAE 161

Query: 129 RKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMI 188
             P +LSGG +QRV + R +  +P + L DE  S LD  +R +M+ EL  L  +   T++
Sbjct: 162 SMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIV 221

Query: 189 YVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFV-AEFIGSPAMNVFSS-DV 246
           +++HD  EAM + D+I ++  GR+ QVG+P ++   P   +V A F G    N+ ++ D+
Sbjct: 222 FISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDI 281

Query: 247 GLQ 249
             Q
Sbjct: 282 ATQ 284


Lambda     K      H
   0.320    0.139    0.396 

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: 330
Number of extensions: 21
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: 338
Length of database: 415
Length adjustment: 30
Effective length of query: 308
Effective length of database: 385
Effective search space:   118580
Effective search space used:   118580
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: 50 (23.9 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