GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gyaR in Pedobacter sp. GW460-11-11-14-LB5

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate CA265_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase

Query= curated2:Q9YAW4
         (335 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS12240 CA265_RS12240
           phosphoglycerate dehydrogenase
          Length = 311

 Score =  187 bits (476), Expect = 2e-52
 Identities = 118/318 (37%), Positives = 173/318 (54%), Gaps = 21/318 (6%)

Query: 3   RPRVFVTREVFPEALELLSKYYDVEVWDKYQPPPYETLLSKAREADALYTLLTDRIDCDL 62
           R  V +   +  EAL LL +  +V V+  Y     +  L+   E  A+ T     ID  L
Sbjct: 2   RKNVLLLETIAEEALALLQE--NVNVFTGYDEAGLKDTLNNV-EVHAIITRGKKHIDKTL 58

Query: 63  LSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRVVE 122
           +   P L + A+  VG DN+DV+ A+   I V N PG      AE T AL+L   R +  
Sbjct: 59  MDACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDMHR 118

Query: 123 ADHFVRWGEW-WRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHS 181
           + + V+   W WR +         G EL GKTLGILG+G IG RVA++G AFGM+++  S
Sbjct: 119 SVNHVKQNNWNWRNQYA-------GDELNGKTLGILGLGNIGKRVAKLGDAFGMKVLCWS 171

Query: 182 RSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNTG 241
           RS           +   L+++L++SD++S+HLPL++ET  +IG S+L LMK  A L+NT 
Sbjct: 172 RS----------VQDLPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTA 221

Query: 242 RGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETRLR 301
           RGA++D  AL+ AL  G IA  A DV  +EP   +  +    N ++ PHAAS T  T  +
Sbjct: 222 RGALIDHAALLDALNAGTIAGFAADVLPDEPPLQSLAVVQHPNALVTPHAASLTASTYKQ 281

Query: 302 MAMMAAENLVAFAQGKVP 319
           M ++   N+++   G+ P
Sbjct: 282 MCLLTVRNVLSVLAGQQP 299


Lambda     K      H
   0.322    0.136    0.406 

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: 228
Number of extensions: 9
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: 335
Length of database: 311
Length adjustment: 28
Effective length of query: 307
Effective length of database: 283
Effective search space:    86881
Effective search space used:    86881
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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