GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Chryseobacterium viscerum 687B-08

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_103235037.1 C1634_RS07230 D-2-hydroxyacid dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_002899945.2:WP_103235037.1
          Length = 319

 Score =  166 bits (420), Expect = 7e-46
 Identities = 113/331 (34%), Positives = 178/331 (53%), Gaps = 46/331 (13%)

Query: 4   KVFITRQIPENGIKMI-EKFYEIELWKDPKAPPRGVLLEKVRE--VDALVTLVTDKVDKE 60
           KV     + ++GI  + EK +E+   K P+      L++ + E  +  L+     +V K+
Sbjct: 2   KVLANDGLDQSGIDALTEKGFEVITTKVPQE----FLVDYINEHKIRTLLVRSATQVRKD 57

Query: 61  LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           +++N P + II +  VG DNID++ A ++GI+V NTP   +++ A+L FA L + AR + 
Sbjct: 58  IIDNCPSIDIIGRGGVGMDNIDVDYAREKGIHVINTPSASSESVAELVFAHLFSGARFLQ 117

Query: 121 EADAFV------RSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGM 174
           +++  +        G  KK+          G  L+GKT+GI+G GRIGQ +A+ A G GM
Sbjct: 118 DSNRKMPLVGDTEFGGLKKAYAA-------GIELRGKTIGIIGMGRIGQEVARIALGLGM 170

Query: 175 KIIYYSRTRKPEAEEEIGAEY------------VDFET-----LLKESDFISLHVPLTKE 217
           +++         A+  IG               VD ET     +LK SDFI+LHVP  K+
Sbjct: 171 RVV--------AADNNIGKASIKVKFYNNQFINVDIETEPLQEVLKHSDFITLHVPAQKD 222

Query: 218 TYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEEL 277
            Y MIG+ E  +MK    ++N SRG V+D  ALI AL  G +  AGLDVF  EP  ++E+
Sbjct: 223 GY-MIGKNEFDMMKDGVAIVNCSRGGVIDETALIHALDSGKVRFAGLDVFINEPTPSKEI 281

Query: 278 FKLKNVVLAPHIGSATHEAREGMAELVAKNL 308
                + L PH G++T EA++ +   +A+ +
Sbjct: 282 LNHSKISLTPHTGASTLEAQDRIGLSLAEQI 312


Lambda     K      H
   0.317    0.137    0.392 

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: 240
Number of extensions: 11
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: 331
Length of database: 319
Length adjustment: 28
Effective length of query: 303
Effective length of database: 291
Effective search space:    88173
Effective search space used:    88173
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: 48 (23.1 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