GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_078430036.1 BK574_RS21465 D-glycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_002019605.1:WP_078430036.1
          Length = 320

 Score =  318 bits (816), Expect = 9e-92
 Identities = 163/316 (51%), Positives = 223/316 (70%), Gaps = 5/316 (1%)

Query: 1   MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60
           MKPKV +TR +P  GI+ + +  ++E+    +   +  L++ + + DA+++L+ +++D E
Sbjct: 1   MKPKVLVTRDLPGEGIERLREVADVEVHTGKEELTKEQLIQAIADKDAIISLLVNEIDAE 60

Query: 61  LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           +++ AP LK+I+ YAVG++NID++ A +RGI VTNTP VLT++TADL +ALLLAVARRI 
Sbjct: 61  VMDAAPHLKVISNYAVGFNNIDVDAAQERGIIVTNTPDVLTESTADLTWALLLAVARRIP 120

Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180
           E+D + R G++    VGW P + LG  + GKTLGI+G GRIG+A+ +RAKGFGM I+YY+
Sbjct: 121 ESDTYTREGKF----VGWAPELLLGRTVYGKTLGIIGMGRIGEAVVRRAKGFGMNIVYYN 176

Query: 181 RTR-KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239
           R     E E E+ A Y   E ++ ++DF+SLH PLT ET ++I E ELK MK  A LINT
Sbjct: 177 RRPLSTEKELELDASYASLEEVISQADFLSLHTPLTPETRYLIDENELKAMKDTAYLINT 236

Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299
           SRG +V+  AL+ ALKE  IAGAGLDVFE EP   EEL   +NVVLAPHIGSAT E R  
Sbjct: 237 SRGPLVNEKALVNALKEKAIAGAGLDVFENEPAIEEELLNFQNVVLAPHIGSATIETRVE 296

Query: 300 MAELVAKNLIAFAKGE 315
           MA+L   N I+  KGE
Sbjct: 297 MADLAINNTISILKGE 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: 295
Number of extensions: 8
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: 331
Length of database: 320
Length adjustment: 28
Effective length of query: 303
Effective length of database: 292
Effective search space:    88476
Effective search space used:    88476
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 Apr 09 2024. 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