GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucD in Caulobacter crescentus NA1000

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate CCNA_01555 CCNA_01555 altronate dehydratase

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__Caulo:CCNA_01555
          Length = 502

 Score =  183 bits (464), Expect = 1e-50
 Identities = 134/408 (32%), Positives = 201/408 (49%), Gaps = 32/408 (7%)

Query: 4   AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP 63
           +A   T +G+ R +GR G RN + V   V C  + AR I  +  +         A R   
Sbjct: 111 SADTRTFQGFRRKNGRAGTRNEIWVLCTVGCVANTARRIAEKANQRF-------AGRVDG 163

Query: 64  VHLIGFP-GCYPNG----YAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGR 118
           V+    P GC   G    +  K++  L +HPN G VL + LGCE+     L++      R
Sbjct: 164 VYAFPHPFGCSQLGDDLAHTRKLIAALASHPNAGGVLILGLGCENNQLKALLESAPDIDR 223

Query: 119 P-VEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGI 177
             ++  T Q        ++ G+  +    E     ++ P+ +SELV+G  CGGSDG SGI
Sbjct: 224 ERLKGFTTQM---VEDELEDGLAAVEALVEIAEKDRREPVPVSELVVGLKCGGSDGFSGI 280

Query: 178 TANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYS 237
           TANP VGR  D + +AG T +  E  E+ G E  +  RAA   + D  VA +    RY+ 
Sbjct: 281 TANPLVGRIADKVAEAGGTPVLTEIPEIFGAENVLLQRAASREVFDAAVAVIDDFKRYFI 340

Query: 238 ILGHGSF---AVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVP 294
                 +   + GN  GG+T+ EEKSLGA  K G +P+V +++ G+     GL LL+   
Sbjct: 341 EANQPIYENPSPGNIAGGITSLEEKSLGAVQKGGRAPLVEVLRYGETVGRHGLTLLEAP- 399

Query: 295 DGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSG 354
                 G   +S  A    L A GA VILFTTGRG+ +G   +P +K+ +N    +   G
Sbjct: 400 ------GNDAVSSTA----LTAAGATVILFTTGRGTPLGFP-APTLKIASNSGLAQRKPG 448

Query: 355 DMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFIL 402
            +D DAG++LEG  ++D     + +  +  + G  +K+E  G +E  L
Sbjct: 449 WIDFDAGQVLEG-VSMDVAAENLMDLVIETASGKTTKAELNGEREIAL 495


Lambda     K      H
   0.318    0.137    0.408 

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: 582
Number of extensions: 29
Number of successful extensions: 6
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: 431
Length of database: 502
Length adjustment: 33
Effective length of query: 398
Effective length of database: 469
Effective search space:   186662
Effective search space used:   186662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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