GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Mesorhizobium ciceri biovar biserrulae WSM1271

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013528159.1 MESCI_RS01435 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000185905.1:WP_013528159.1
          Length = 311

 Score =  195 bits (495), Expect = 1e-54
 Identities = 107/262 (40%), Positives = 158/262 (60%), Gaps = 9/262 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL ++ +S+ FGG++A+ D     ++G+I A+IGPNGAGK+++ N I+G Y+P  G +  
Sbjct: 52  LLSLQGISLSFGGVVALADIDLSVRQGEIRAIIGPNGAGKSSLINVISGVYRPDRGHVQL 111

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           +  S  Q   +RL          VARTFQN+ LF GL+VL+N+      K+       +L
Sbjct: 112 DGTSYAQVPTQRLAHLG------VARTFQNLALFKGLSVLDNVASGLAYKVRSNFAGQVL 165

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           G   +G  + E  ++   A   LE   L    D   G LPYG Q+R+E+ARA+   P LL
Sbjct: 166 G---IGRSRGEQRDSRSRAEQILEFLHLTAIRDRLVGTLPYGLQKRVELARALVAEPRLL 222

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEP AG+   E + + + +++ R    T+++LIEHD+ VVM +SD + VL+YG+KI+D
Sbjct: 223 LLDEPMAGMTASEKSEMASFVRAARDRFATTVVLIEHDVGVVMGLSDRIAVLDYGRKIAD 282

Query: 254 GTPDHVKNDPRVIAAYLGVEDE 275
            TPD V+ND RVI AYLGV  +
Sbjct: 283 ATPDEVRNDQRVIDAYLGVASD 304


Lambda     K      H
   0.318    0.136    0.386 

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: 228
Number of extensions: 12
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: 292
Length of database: 311
Length adjustment: 27
Effective length of query: 265
Effective length of database: 284
Effective search space:    75260
Effective search space used:    75260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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