GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Sporolactobacillus vineae SL153

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_010632401.1 RH97_RS10960 SDR family oxidoreductase

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>NCBI__GCF_000246965.1:WP_010632401.1
          Length = 271

 Score =  318 bits (816), Expect = 6e-92
 Identities = 166/271 (61%), Positives = 199/271 (73%), Gaps = 4/271 (1%)

Query: 1   MNTWLNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQ----SSGNYNFW 56
           M+ WL L  + + VTGG+SGIG A+V  LL   ANV + D+   D       S G   F 
Sbjct: 1   MSNWLGLDHQTVIVTGGSSGIGRAVVQTLLENQANVVVADLQEPDHETYEKGSEGQLLFV 60

Query: 57  PTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMV 116
            T+++S   V   V   ++ FG+++ LVNNAG+N PRLLVD K P G +EL++   +KM+
Sbjct: 61  KTNVASRESVENLVGQAVKNFGKVNVLVNNAGINLPRLLVDAKEPGGHFELSDDVLDKMI 120

Query: 117 NINQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSK 176
           +INQKGVFL SQ   R+MVK + GVIVN+ SESGLEGSEGQS YAATKAAL SFTRSW+K
Sbjct: 121 SINQKGVFLCSQIAGREMVKAQKGVIVNMVSESGLEGSEGQSGYAATKAALYSFTRSWAK 180

Query: 177 ELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLT 236
           ELGK  IRVVGVAPGILEKTGLRTP YEEALA+TR ITVEQLR+GY+  SIPL R G+L 
Sbjct: 181 ELGKFNIRVVGVAPGILEKTGLRTPAYEEALAYTRGITVEQLRKGYTNKSIPLRRDGKLK 240

Query: 237 EVADFVCYLLSERASYMTGVTTNIAGGKTRG 267
           EVAD V YL S+RASY+TG T NIAGGK+RG
Sbjct: 241 EVADLVAYLSSDRASYITGTTYNIAGGKSRG 271


Lambda     K      H
   0.315    0.132    0.378 

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: 237
Number of extensions: 5
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: 267
Length of database: 271
Length adjustment: 25
Effective length of query: 242
Effective length of database: 246
Effective search space:    59532
Effective search space used:    59532
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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