GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Gallaecimonas xiamenensis 3-C-1

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_008485733.1 B3C1_RS14495 D-glycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_000299915.1:WP_008485733.1
          Length = 337

 Score =  249 bits (637), Expect = 5e-71
 Identities = 148/329 (44%), Positives = 205/329 (62%), Gaps = 10/329 (3%)

Query: 1   MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60
           MKP+VF+  ++    +  +E  Y++    DPK   +G     +  V  ++ +     + E
Sbjct: 1   MKPQVFVFSRLKPPFLAELEAHYQVTQL-DPKGDIQGQYAAALPHVQGMIGVGRPLGEAE 59

Query: 61  LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           L + A +LK+I+  +VGYDN D+     R I +TNTP VLT+ TADL FALL++ ARR+ 
Sbjct: 60  LAQ-AGQLKVISSVSVGYDNYDLPYLNSRSIMLTNTPDVLTETTADLGFALLMSAARRLP 118

Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKIIYY 179
           E DA+V++G+W+++ VG  P  F G  + GKTLGIVG GRIG ALA+R   GF M ++Y 
Sbjct: 119 ELDAWVKAGQWQRT-VG--PAEF-GVDIHGKTLGIVGLGRIGAALARRGHFGFRMPVLYS 174

Query: 180 SRTR---KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAIL 236
             +R   KPE E E+GA ++  + LL ++DF+ L VPL  ET ++IG +EL LMK +AIL
Sbjct: 175 GNSRNSRKPELEAELGARFLPLDDLLAQADFVVLVVPLGPETRNLIGRRELALMKDSAIL 234

Query: 237 INTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEA 296
           +N +RGAVVD  ALI+AL+   I GAGLDV++ EP     LF L  VV  PH+GSAT E 
Sbjct: 235 VNLARGAVVDEPALIEALQSRQIRGAGLDVYQTEPLAASPLFALPQVVTLPHLGSATEET 294

Query: 297 REGMAELVAKNLIAFAKGEIPPNLVNKDV 325
           R+ MA     N     KGE P +LVN  V
Sbjct: 295 RDAMARRALDNFHQAMKGERPRDLVNPQV 323


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: 270
Number of extensions: 10
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: 337
Length adjustment: 28
Effective length of query: 303
Effective length of database: 309
Effective search space:    93627
Effective search space used:    93627
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