GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Carboxydothermus pertinax Ug1

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_075858559.1 cpu_RS03150 phosphoglycerate dehydrogenase

Query= curated2:A1RYE4
         (339 letters)



>NCBI__GCF_001950255.1:WP_075858559.1
          Length = 525

 Score =  230 bits (587), Expect = 5e-65
 Identities = 133/312 (42%), Positives = 202/312 (64%), Gaps = 9/312 (2%)

Query: 12  IPEPGLSMLKECCDVVVHESKDWPPSREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLK 71
           + E GL++L+E   +V  ++K    S EEL++ I + DAL+     K+ A +++AA NLK
Sbjct: 9   VSEKGLNILREEGFIVEEKTK---LSEEELIKIISEFDALIVRSETKVTARIIEAAENLK 65

Query: 72  VISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVEADKIIRTG 131
           +I    VG D+ID+  A+K+GI V ++P   T A AE T  L++A+ R I +A   ++ G
Sbjct: 66  IIGRAGVGVDNIDLAAASKKGIIVVNSPEGNTIAAAEHTFALMMALLRNIPQAHAALKEG 125

Query: 132 QWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVIP 191
           +W +       TG EL+GKT+G++GLGRIG A AKR+ +F+ K++ YD     +   ++ 
Sbjct: 126 KWLRKE----FTGYELRGKTVGIIGLGRIGTAVAKRVKAFETKVIGYDPFISEERAHML- 180

Query: 192 NMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARGPVVDTEALV 251
            +    L+ LL+K+DIV++H+PL  ET +LIN ERL+ MKK+A++IN ARG ++D EAL 
Sbjct: 181 GITLMSLEELLQKADIVTMHLPLNNETRNLINRERLKLMKKSAFIINCARGGIIDEEALY 240

Query: 252 KALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEARQRMAELAARNLIA 311
           +ALK G IAGAALDVF +EPL  + PL +  NV++ PH+ ++T EA+  +A   AR +  
Sbjct: 241 EALKTGEIAGAALDVFSKEPLTES-PLFELPNVIVTPHLGASTKEAQVNVAIDVAREIAN 299

Query: 312 VLKGEMPPALVN 323
           VLKG +    VN
Sbjct: 300 VLKGGLAQNAVN 311


Lambda     K      H
   0.319    0.137    0.404 

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: 410
Number of extensions: 19
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: 339
Length of database: 525
Length adjustment: 32
Effective length of query: 307
Effective length of database: 493
Effective search space:   151351
Effective search space used:   151351
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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