GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Vagococcus penaei CD276

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_077276299.1 BW732_RS08225 SDR family oxidoreductase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>NCBI__GCF_001998885.1:WP_077276299.1
          Length = 259

 Score =  117 bits (293), Expect = 2e-31
 Identities = 85/252 (33%), Positives = 129/252 (51%), Gaps = 12/252 (4%)

Query: 14  RVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAID----RARTAHPQLHAGVADVSDC 69
           RV+I+GA +GIG A A  F ++GA V + D++   +D         + + +  V DV D 
Sbjct: 8   RVVITGAGSGIGRATALKFAELGAVVGLIDINEQGLDDIVKEIYRHNGEAYYEVVDVMDE 67

Query: 70  AQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAV 129
            ++   I    ++LGGLD L+ NAGI G    +E L   +W RTI TNL S F  L+ A+
Sbjct: 68  ERLMEGIAQLANQLGGLDGLVCNAGINGTWAPIETLKIEDWHRTIDTNLTSTFVSLKAAI 127

Query: 130 PLLKETSANPGIIAMASVAGRLGY--AFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187
           PL+K+   +  I+  +S+ G   Y     + Y+ SK   V ++K  A+EL   N+RVNA+
Sbjct: 128 PLMKDDGGS--IVITSSINGNRIYNNFGASAYSTSKAGQVSLMKMAALELARCNIRVNAV 185

Query: 188 LPGVVEGE-RMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246
            PG +E       +I    E + I  +  +G+   K    +   V +V A   FL S   
Sbjct: 186 CPGAIETPINSKTIIEKETEEVQIKVEFPEGDRPLKADTGQPEQVANVIA---FLISSQS 242

Query: 247 QNISGQAISVDG 258
            N+SG  + VDG
Sbjct: 243 GNVSGTEVYVDG 254


Lambda     K      H
   0.320    0.136    0.391 

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: 146
Number of extensions: 4
Number of successful extensions: 3
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: 263
Length of database: 259
Length adjustment: 25
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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