GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucD in Pedobacter sp. GW460-11-11-14-LB5

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate CA265_RS04670 CA265_RS04670 altronate hydrolase

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



>FitnessBrowser__Pedo557:CA265_RS04670
          Length = 545

 Score =  138 bits (348), Expect = 4e-37
 Identities = 98/330 (29%), Positives = 154/330 (46%), Gaps = 19/330 (5%)

Query: 80  KMLERLTTHPNVGAVLFVSLGCESMN----KHYLVDVVRASGRPVEVLTIQEKGGTRSTI 135
           K+L     HPNV  +  +SLGC+ +     K  L  +     +P+ +   Q+       I
Sbjct: 219 KLLAAYAHHPNVAGITVLSLGCQHLQVEDFKRDLFALDPDFDKPLLIFEQQKAQSEEELI 278

Query: 136 QYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGA 195
           Q  +         +  Q +    LS++ +G  CGGSDG SGI+ANP+VG   D L+  GA
Sbjct: 279 QNSIRSTFEGLMFINKQARAAAPLSKMCVGVKCGGSDGFSGISANPSVGYCADLLVALGA 338

Query: 196 TCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHGSF---AVGNADGG 252
             +  E  EL G E  M  R+      ++ +  + +       +G G +   + GN   G
Sbjct: 339 KVLLAEFPELCGVEQEMIDRSVDQPTAEKFIRLMTEYDDLAHKVGSGFYMNPSPGNIKDG 398

Query: 253 LTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIG 312
           L T   KS GA  K+G++PIV ++   +     GL L+            P     A  G
Sbjct: 399 LITDAIKSAGAARKAGSAPIVDVLDYTEPATKPGLSLVCT----------PGNDVEATTG 448

Query: 313 ELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDE 372
           +  A GA +ILFTTG G+  G+ + P IKV  N    + +S  +D+D G ++ G  T++E
Sbjct: 449 KA-AAGATLILFTTGLGTPTGNPVCPTIKVATNSILAKRMSDIIDIDTGAVINGEKTINE 507

Query: 373 VGREVFEQTVAVSRG-AASKSETLGHQEFI 401
           +G ++ E  + V+ G    K+  L   +FI
Sbjct: 508 MGEDILEYCIKVASGEEIPKAVQLNQDDFI 537


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: 592
Number of extensions: 36
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: 431
Length of database: 545
Length adjustment: 34
Effective length of query: 397
Effective length of database: 511
Effective search space:   202867
Effective search space used:   202867
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: 52 (24.6 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