GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Flavobacterium glycines Gm-149

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_066330061.1 BLR17_RS12115 3-phosphoglycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_900100165.1:WP_066330061.1
          Length = 316

 Score =  162 bits (411), Expect = 8e-45
 Identities = 115/326 (35%), Positives = 174/326 (53%), Gaps = 33/326 (10%)

Query: 4   KVFITRQIPENGIKMIEKF-YEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELL 62
           KV     I ++GI  +EK  +E+   K  +      + E    V  ++     KV K+++
Sbjct: 2   KVLANDGISKSGILALEKGGFEVITTKVAQEQVANFVNEN--NVSVVLVRSATKVRKDII 59

Query: 63  ENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVAR----- 117
           +  P LKII +  VG DNID++ A  +GI+V NTP   +++ A+L FA LL   R     
Sbjct: 60  DACPGLKIIGRGGVGMDNIDVDYAKSKGIHVINTPASSSESVAELVFAHLLTGVRFLHDS 119

Query: 118 -RIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKI 176
            R +  +   +  + KK+          G  L+GKTLGIVG GRIGQA AK A G GMK+
Sbjct: 120 NRNMPLEGDTKFNDLKKAYAN-------GVELRGKTLGIVGIGRIGQATAKMALGLGMKV 172

Query: 177 IYYSRTRKPEAEEEIGAEYVD------------FETLLKESDFISLHVPLTKETYHMIGE 224
           I  + +  P+ + ++  E+ D             E++  ESDFI+LHVP   +  +++ E
Sbjct: 173 IA-ADSFIPQVDVKV--EFFDGQSITTTIKTQSLESVFAESDFITLHVPA--QNGYIVTE 227

Query: 225 KELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVV 284
           KE   MK    ++N +RG V++   L+KAL  G +A AGLDVFE EP    +L     + 
Sbjct: 228 KEFATMKNGVGIVNCARGGVINEVDLVKALDSGKVAFAGLDVFENEPTPATQLLMHPKIS 287

Query: 285 LAPHIGSATHEAREGMAELVAKNLIA 310
           L PHIG+AT EA++ +   +A  +I+
Sbjct: 288 LTPHIGAATGEAQDRIGTELASQIIS 313


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: 256
Number of extensions: 9
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: 316
Length adjustment: 28
Effective length of query: 303
Effective length of database: 288
Effective search space:    87264
Effective search space used:    87264
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