GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Cupriavidus basilensis 4G11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS16960 RR42_RS16960 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Cup4G11:RR42_RS16960
          Length = 238

 Score =  355 bits (911), Expect = e-103
 Identities = 180/236 (76%), Positives = 208/236 (88%)

Query: 7   KVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNI 66
           + LL++ GLKVAYGGIQAVKG+D E++EGELV+LIG+NGAGKTTTMKAITG      G++
Sbjct: 3   ETLLKISGLKVAYGGIQAVKGIDLEIKEGELVTLIGANGAGKTTTMKAITGLQGWAGGDV 62

Query: 67  EYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMF 126
           EY+GKSIKG  ++ L+K+GL MVPEGRGVFARMTITENLQMGAY R D+AGI ADI++MF
Sbjct: 63  EYMGKSIKGVPSYTLLKQGLAMVPEGRGVFARMTITENLQMGAYTRTDEAGIKADIDRMF 122

Query: 127 TIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVR 186
            IFPRL+ER +QLAGTMSGGEQQMLAM RALMSQPK+LLLDEPSMGLSPIMV KIFEVVR
Sbjct: 123 GIFPRLKERANQLAGTMSGGEQQMLAMARALMSQPKLLLLDEPSMGLSPIMVAKIFEVVR 182

Query: 187 DVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242
           DV ALGVT++LVEQNA  AL  A RGYVMESGL+TM+G  +Q+L+DPKVRAAYLGE
Sbjct: 183 DVSALGVTVLLVEQNARLALQAAHRGYVMESGLVTMSGDAKQMLDDPKVRAAYLGE 238


Lambda     K      H
   0.317    0.136    0.373 

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: 252
Number of extensions: 3
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: 242
Length of database: 238
Length adjustment: 23
Effective length of query: 219
Effective length of database: 215
Effective search space:    47085
Effective search space used:    47085
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: 46 (22.3 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