GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS12240
          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.

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