GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Cupriavidus basilensis 4G11

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS16965 RR42_RS16965 ABC transporter

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Cup4G11:RR42_RS16965
          Length = 258

 Score =  192 bits (487), Expect = 9e-54
 Identities = 116/266 (43%), Positives = 158/266 (59%), Gaps = 18/266 (6%)

Query: 10  SDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMG 69
           +++ LL V+ ++ +FGGL A++D   + K G+I  LIGPNGAGKTT FN ITG Y P  G
Sbjct: 3   NENLLLSVQGVNKRFGGLQALSDVGLQIKPGEIYGLIGPNGAGKTTFFNVITGLYTPDSG 62

Query: 70  MITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129
                   GK Y    + +     +A +ARTFQNIRLF  +T LEN++V +H +      
Sbjct: 63  EFVL---GGKAYQPTAVHE---VAKAGIARTFQNIRLFGEMTALENVMVGRHVR------ 110

Query: 130 YTILGLIGV----GPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARA 185
            T  GL G        +RE     + A   LE   +   A   + +L YG QRRLEIARA
Sbjct: 111 -TKAGLFGAVFRPPSVRREEHSVEDWAHDLLEYVGIGKYAHFTSRNLSYGHQRRLEIARA 169

Query: 186 MCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVL 245
           + T P+LL LDEPAAG+N  E   L  LL  IR++ G +ILLIEHD+ +VM + + + VL
Sbjct: 170 LATEPKLLALDEPAAGMNATEKVELRGLLDKIRSD-GKTILLIEHDVKLVMGLCNRLTVL 228

Query: 246 EYGQKISDGTPDHVKNDPRVIAAYLG 271
           +YG+ I+ G P  V+++P VI AYLG
Sbjct: 229 DYGKVIAQGLPHEVQSNPAVIEAYLG 254


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: 207
Number of extensions: 12
Number of successful extensions: 4
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: 258
Length adjustment: 25
Effective length of query: 267
Effective length of database: 233
Effective search space:    62211
Effective search space used:    62211
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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