GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Caulobacter crescentus NA1000

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate CCNA_01575 CCNA_01575 glucose / sorbosone dehydrogenase

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Caulo:CCNA_01575
          Length = 408

 Score =  173 bits (438), Expect = 8e-48
 Identities = 123/356 (34%), Positives = 180/356 (50%), Gaps = 41/356 (11%)

Query: 14  GLARGQGLRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLF-REGRLS-TYAELP-VY 70
           GL  G   + + +  GLE PW +AFLP G +L+ ER GR+R+  ++G+LS     LP +Y
Sbjct: 55  GLVSGVSGQYQTLASGLEHPWGMAFLPSGEILVTERAGRLRVVGKDGKLSPAVTGLPAIY 114

Query: 71  HRGESGLLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLR-HLGERGVLD--RVVLDG 126
             G+ GLLG+ L P + +   VY AY    +      V R +  LG    ++  +V+   
Sbjct: 115 AEGQGGLLGVTLDPDYAKNGLVYWAYAEEIDSVNGTAVARGKLTLGAAPKVENVQVIWRQ 174

Query: 127 IPARPHGLHSGGRIAFGPDGMLYVTTGE-VYE--RELAQDLASLGGKILRLTPEGEPAPG 183
            P     LH GGR+ F   G L++TTGE  Y   R  +Q+L    GK++R+  +G     
Sbjct: 175 TPKMASPLHFGGRVVFDRAGKLFITTGERAYPAGRVQSQNLDGTLGKVVRINADGSIPSD 234

Query: 184 NPFLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNY 243
           NPF+   GA+P+++SLGHRN Q  A     G L++ EHG       G DE+N   PG NY
Sbjct: 235 NPFVNTAGAKPDIWSLGHRNIQS-ATLDAQGRLWTVEHG-----ARGGDELNRPEPGKNY 288

Query: 244 GWPRVV------------GRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVA 283
           GWP +             G         P+Y+W     P  +A +        +G L + 
Sbjct: 289 GWPLITYGEEYSGKAISDGATQKEGLEQPVYYWDPVIAPSGMALYDGALFPALKGSLLIG 348

Query: 284 GLRGQALLRLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDGR 338
            +R Q + RLVL+ +    +V+  E   +   GR+R+V VGPDGA+YV T   DG+
Sbjct: 349 SMREQHVARLVLKDD----KVVGEERLFTDIGGRVRDVAVGPDGAIYVLTDEGDGK 400


Lambda     K      H
   0.322    0.146    0.460 

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: 542
Number of extensions: 37
Number of successful extensions: 7
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: 352
Length of database: 408
Length adjustment: 30
Effective length of query: 322
Effective length of database: 378
Effective search space:   121716
Effective search space used:   121716
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 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