GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Sinorhizobium meliloti 1021

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate SMc02849 SMc02849 2-hydroxyacid dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__Smeli:SMc02849
          Length = 334

 Score =  269 bits (687), Expect = 8e-77
 Identities = 151/328 (46%), Positives = 208/328 (63%), Gaps = 12/328 (3%)

Query: 2   KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61
           KP V+ITR++P+     + + ++ EL  D     +  L+  V+  D LV  VTD++D  L
Sbjct: 6   KPTVYITRKLPDVVETRMRELFDAELNIDDTPRSQPELVAAVKRADVLVPTVTDRIDAAL 65

Query: 62  LENA-PKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           +E A P+LK+IA ++ G DNID++ A ++GI VTNTP VLT+ TAD+  AL+LAV RR+ 
Sbjct: 66  IEQAGPQLKLIAAFSNGVDNIDVDAAARKGITVTNTPNVLTEDTADMTMALILAVPRRLA 125

Query: 121 EADAFV--RSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIY 178
           E    +  R GEW     GW P   LG  + GK +GIVG GRIG A+A+RAK FG+ I Y
Sbjct: 126 EGAQVLTDRKGEW----AGWSPTWMLGRRIAGKRIGIVGMGRIGTAVARRAKAFGLSIHY 181

Query: 179 YSRTR-KPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAIL 236
           ++R R KPE EE + A Y D  + +L   D +S++ P T  TYH++  + L LM+P++ +
Sbjct: 182 HNRHRVKPETEEMLEATYWDSLDQMLARVDIVSVNCPSTPATYHLLSARRLALMRPDSYI 241

Query: 237 INTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLK---NVVLAPHIGSAT 293
           +NT+RG ++D  ALIK+L+EG IAGAGLDVFE EP  N +L KL     VVL PH+ SAT
Sbjct: 242 VNTARGGIIDEAALIKSLREGKIAGAGLDVFENEPCVNPKLIKLAGEGKVVLLPHMSSAT 301

Query: 294 HEAREGMAELVAKNLIAFAKGEIPPNLV 321
            E R  M E V  N+  F  G  PP+ V
Sbjct: 302 LEGRIDMGEKVVINIRTFFDGHRPPDRV 329


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: 289
Number of extensions: 11
Number of successful extensions: 5
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: 334
Length adjustment: 28
Effective length of query: 303
Effective length of database: 306
Effective search space:    92718
Effective search space used:    92718
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 17 2021. 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