GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas stutzeri RCH2

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate GFF3163 Psest_3223 Lactate dehydrogenase and related dehydrogenases

Query= curated2:B1L765
         (332 letters)



>FitnessBrowser__psRCH2:GFF3163
          Length = 319

 Score =  171 bits (433), Expect = 2e-47
 Identities = 105/280 (37%), Positives = 164/280 (58%), Gaps = 14/280 (5%)

Query: 39  IIERVKDCD-ALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTP 97
           I+ER++    A+V+ ++  + AE   A P+L+++   A G +NID++ A +RGI V+N  
Sbjct: 41  IVERLQGAQVAIVNKVS--LTAETLAACPELKLILVSATGVNNIDLQAARERGIVVSNCQ 98

Query: 98  GVLTETTADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVY---GRTLGIVG 154
              T T A     LL+A A R+ +    V  G+W+ +     +L + +    G+TLG++G
Sbjct: 99  AYGTPTVAQHTLMLLLALATRLPDYQAAVARGRWQESGQ-FCLLDFPIVELEGKTLGLLG 157

Query: 155 MGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEE 214
            G +G+AVAR A+ FGMR+L  +   R    + L      L++LL + D ++LH PLTE+
Sbjct: 158 HGELGSAVARLAEAFGMRVLVGNLPGRPKRPERLD-----LDELLPQVDALTLHCPLTEQ 212

Query: 215 TYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDP 274
           T ++IG  +L+ MK TA L+N +RG +VD++AL  AL+ G + GA  DV   EP   D+P
Sbjct: 213 TRNLIGARELQLMKPTAFLINAARGGLVDEQALADALRRGHLGGAATDVLTSEPPRDDNP 272

Query: 275 LL--KLENVVLAPHAASASHETRSRMAEMVAENLIAFKRG 312
           LL   L  +++ PH+A  S E R R+   +AEN  AF  G
Sbjct: 273 LLAPDLPRLIITPHSAWGSREARQRIVAQLAENATAFFAG 312


Lambda     K      H
   0.319    0.137    0.398 

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: 216
Number of extensions: 9
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: 332
Length of database: 319
Length adjustment: 28
Effective length of query: 304
Effective length of database: 291
Effective search space:    88464
Effective search space used:    88464
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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