GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Caulobacter crescentus NA1000

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate CCNA_02230 CCNA_02230 gluconate 2-dehydrogenase

Query= curated2:Q9YAW4
         (335 letters)



>FitnessBrowser__Caulo:CCNA_02230
          Length = 319

 Score =  144 bits (364), Expect = 2e-39
 Identities = 101/317 (31%), Positives = 159/317 (50%), Gaps = 13/317 (4%)

Query: 2   KRPRVFVTREVFPEALELLSKYYDVE-VWDKYQPPPYETLLSKAREADALYTLLTDRIDC 60
           ++P++ ++ E+      LL   Y V  +WD   P     L    +   A+       +  
Sbjct: 7   EKPQILLSHEMLMPLQPLLEGAYIVHRLWD--YPDRMAFLEGPGQSIRAIVHAGEMALSR 64

Query: 61  DLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRV 120
           D+L++ PRL ++A ++VG+D +DV      GI VT++ G+     A+    L+LAA R +
Sbjct: 65  DMLAEMPRLGLIACVSVGYDGVDVPWCKAHGIAVTHSTGLNAADVADHAVGLVLAAWRGI 124

Query: 121 VEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYH 180
           VE D  +R G W          M     LRG+  G++G+G IG  VA   KAF M++ + 
Sbjct: 125 VEGDQRLRGGHWSHAER-----MAPRPGLRGRKAGVVGLGHIGEAVAARLKAFDMKVAWW 179

Query: 181 SRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNT 240
           +  R +E +        SL  L R+SD+L +     D  RHLI +  ++ +    ++VN 
Sbjct: 180 A-PRPKETDYPRAD---SLMALARDSDVLIVCARPDDSNRHLINKPVIEAVGAQGLIVNV 235

Query: 241 GRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETRL 300
            RG+++D  AL++ALR G +  AALDVFE+EP  P          VL PH A AT ++  
Sbjct: 236 ARGSLIDEDALIQALRAGTLGMAALDVFEQEP-TPAARWADVPRTVLTPHTAGATLDSLP 294

Query: 301 RMAMMAAENLVAFAQGK 317
            M  +  ENL  +  G+
Sbjct: 295 AMVSLTLENLRRYFHGE 311


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: 243
Number of extensions: 9
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: 335
Length of database: 319
Length adjustment: 28
Effective length of query: 307
Effective length of database: 291
Effective search space:    89337
Effective search space used:    89337
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 (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