GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Malonomonas rubra DSM 5091

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

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  158 bits (399), Expect = 3e-43
 Identities = 95/275 (34%), Positives = 148/275 (53%), Gaps = 15/275 (5%)

Query: 13  YGEVETLKGIDIA---LESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVLG 69
           + + ET  G+  A   +  GE  V++G SG GKST++ ++  L EP+ G +LI    ++ 
Sbjct: 37  FEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVA 96

Query: 70  VHP------KDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123
           ++       +   ++MVFQS+AL P+++V +N  FGLEM  V +   ++        + +
Sbjct: 97  MNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGL 156

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
           E   +  P +LSGG +QRV + R L  +P + L DE  S LD  +R EM+ EL +L    
Sbjct: 157 EAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKA 216

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYV-AGFVGSPPMNIL 242
           + T+V+++HD  EAM +  RIA+M  GR+ Q+  P+E+   PA  YV A F G  P NIL
Sbjct: 217 KRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNIL 276

Query: 243 DAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVK 277
            A   A   ++      +P+    N  A   R VK
Sbjct: 277 TAGDIATQTQV-----TIPITDGKNPRAGLQRLVK 306


Lambda     K      H
   0.320    0.136    0.385 

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: 343
Number of extensions: 15
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: 360
Length of database: 415
Length adjustment: 30
Effective length of query: 330
Effective length of database: 385
Effective search space:   127050
Effective search space used:   127050
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