GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Megamonas funiformis YIT 11815

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_008540147.1 HMPREF9454_RS12055 hydroxyacid dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_000245775.1:WP_008540147.1
          Length = 326

 Score =  196 bits (498), Expect = 7e-55
 Identities = 115/315 (36%), Positives = 180/315 (57%), Gaps = 13/315 (4%)

Query: 4   KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63
           KV I+ ++ ++G+ ++E+     +  +   P    +L ++ + D L+  +   +D+E + 
Sbjct: 3   KVVISHKLHDDGMAVLERAGANVVITNSGKPKD--MLPELLDADGLIIRI-GSIDRETML 59

Query: 64  NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123
               LK+I +  VG D++D+E AT+ GI V   PG  T + A+ A A++ A A+ +V  D
Sbjct: 60  KCKNLKVIGRPGVGVDDVDVEAATELGIPVVIAPGANTRSVAEHAMAMMFACAKDMVRCD 119

Query: 124 AFVRSGEWK-KSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRT 182
             +R G +  +SE       +  Y L GK LG++G G IG  LA+ A G GMK++ Y   
Sbjct: 120 KEMRKGNFAIRSE-------YKAYELNGKVLGLIGCGHIGNILAEMATGIGMKVLVYDPF 172

Query: 183 RKPEAEEEIGAEY-VDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241
            K E  E  G  Y  + E +LKE+D +S+H PLT +T +MIGEKELKLMK   ILIN +R
Sbjct: 173 VKAEVVEAKGYGYRAEMEDILKEADVVSIHTPLTPKTKNMIGEKELKLMKSTGILINCAR 232

Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSATHEAREGM 300
           G +++  AL KAL E WI  A  DV   EP   ++ LF  +N+++ PH+   T EA  G+
Sbjct: 233 GGIINEEALCKALSENWIHSAATDVVVHEPISVDDPLFMHENIIVTPHMAGQTKEAASGV 292

Query: 301 AELVAKNLIAFAKGE 315
           A + A+ ++A   G+
Sbjct: 293 ATMAAEGVMAVINGQ 307


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: 265
Number of extensions: 16
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: 326
Length adjustment: 28
Effective length of query: 303
Effective length of database: 298
Effective search space:    90294
Effective search space used:    90294
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: 49 (23.5 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