GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Cupriavidus basilensis 4G11

Align Lactate utilization protein A (characterized)
to candidate RR42_RS07430 RR42_RS07430 Fe-S oxidoreductase

Query= SwissProt::Q81GA5
         (239 letters)



>FitnessBrowser__Cup4G11:RR42_RS07430
          Length = 241

 Score =  201 bits (510), Expect = 1e-56
 Identities = 101/237 (42%), Positives = 146/237 (61%), Gaps = 2/237 (0%)

Query: 1   MKVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMK 60
           M+V LF TCLVD+    +G + +++LE+ G E+  PEAQ CCGQPAYNSG   A++   +
Sbjct: 1   MRVGLFATCLVDLMRPEIGFSVLKLLEKAGFEVMVPEAQTCCGQPAYNSGERTASRGLAE 60

Query: 61  HMIETFEDAEYIVTPSGSCATM-FHEYPHVFKDDPKWAKRAQKVADKTYEFTQFIVDVLK 119
             +  FE  +Y+V PSGSC  M  H Y  +  DDP+   R + +  + +E T F+V+V K
Sbjct: 61  KFLREFEMFDYVVIPSGSCGGMVLHHYADLLGDDPELNGRYEGLRSRVFELTDFLVNVAK 120

Query: 120 VTDVGASLPGIATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFGGTFSV 179
           + +  +   G  T H SC   R LGVK  P  LL+ + G+ + ++ + + CCGFGGTFSV
Sbjct: 121 LGEFDSKFTGRITYHDSCSGLRELGVKSQPRALLAQLPGVQLSEMKDCEACCGFGGTFSV 180

Query: 180 KMTPISEQMVDEKVDSVMETGADYLIGADCGCLLNIGGRIERLG-KEVKVMHIAEVL 235
           K   IS  +VDEK  ++  +GAD ++  D GC+LNI GR+ R G    +V+HIA+VL
Sbjct: 181 KYGNISTAIVDEKCANIKASGADAVVLGDLGCMLNIEGRLRRTGDTRTQVLHIAQVL 237


Lambda     K      H
   0.320    0.135    0.407 

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: 196
Number of extensions: 8
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: 239
Length of database: 241
Length adjustment: 23
Effective length of query: 216
Effective length of database: 218
Effective search space:    47088
Effective search space used:    47088
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: 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