GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Herbaspirillum seropedicae SmR1

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase

Query= curated2:P37079
         (267 letters)



>FitnessBrowser__HerbieS:HSERO_RS02925
          Length = 244

 Score =  120 bits (301), Expect = 3e-32
 Identities = 87/259 (33%), Positives = 128/259 (49%), Gaps = 32/259 (12%)

Query: 9   DNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYHFWSTDISSATEVQQ 68
           D V +VTGG  GIG AI   L + GA V + D H    H     Y   S DI+ A  V Q
Sbjct: 12  DCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQH----HDAASPYRQQSIDITDAPAVMQ 67

Query: 69  TIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFMSQ 128
               ++    RID L+NNAG   P + +DE      Y++ E  + ++V +N  GVF   +
Sbjct: 68  AAQELLADTGRIDFLINNAGYAGPTVPLDE------YDVGE--WHRIVQVNLLGVFHACR 119

Query: 129 AVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVVGV 188
           +V   M   R G IVN++S +G EG+   S Y+A KA + + T+S  KEL + G+ V  +
Sbjct: 120 SVTPAMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVLVNAI 179

Query: 189 APGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAI---PIGRAGKLSEVADFVCYL 245
           AP  + KT L                + Q+   + +  I   P+ R G + EVAD   +L
Sbjct: 180 APAAV-KTAL----------------LGQMSPAHVQTMIAKSPMHRLGSVDEVADMCAWL 222

Query: 246 LSARASYITGVTTNIAGGK 264
            S   S+ TG   +++GG+
Sbjct: 223 CSGSCSFNTGAVFDLSGGR 241


Lambda     K      H
   0.316    0.133    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: 147
Number of extensions: 6
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: 267
Length of database: 244
Length adjustment: 24
Effective length of query: 243
Effective length of database: 220
Effective search space:    53460
Effective search space used:    53460
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 (21.6 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