GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Pedo557:CA265_RS20005
          Length = 259

 Score =  226 bits (575), Expect = 5e-64
 Identities = 127/255 (49%), Positives = 168/255 (65%), Gaps = 3/255 (1%)

Query: 1   MELNNVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEK 60
           M   N+I E +  +  VTINR KALNALN DTL E+  VI       EV  VILTGAGEK
Sbjct: 1   MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60

Query: 61  SFVAGADISEMKEMNTIEGRKFGILGNK-VFRRLELLEKPVIAAVNGFALGGGCEIAMSC 119
           +FVAGADI E  + +  +G +    G++ VF  +E   KP IAA+NGFALGGG E+AM+C
Sbjct: 61  AFVAGADIKEFSDYSGKQGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELAMAC 120

Query: 120 DIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLV 179
            IRIAS NA+ G PEV LG+ PG+GGTQRL++LVG G A ++I TA  I A +A +IGLV
Sbjct: 121 HIRIASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIGLV 180

Query: 180 NKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFST 239
           N VV  ++L+  A+E+ N I   AP+A+  + +++   +  +     A E E FG+CF T
Sbjct: 181 NVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASI--NNTNGYATEIEEFGKCFET 238

Query: 240 EDQKDAMTAFIEKRK 254
            D K+ +TAF+EKRK
Sbjct: 239 ADFKEGVTAFVEKRK 253


Lambda     K      H
   0.317    0.134    0.365 

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: 225
Number of extensions: 13
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: 261
Length of database: 259
Length adjustment: 24
Effective length of query: 237
Effective length of database: 235
Effective search space:    55695
Effective search space used:    55695
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 (21.6 bits)
S2: 47 (22.7 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