GapMind for catabolism of small carbon sources

 

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

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__Pedo557:CA265_RS20005
          Length = 259

 Score =  177 bits (449), Expect = 2e-49
 Identities = 107/261 (40%), Positives = 150/261 (57%), Gaps = 11/261 (4%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59
           MAY+N++ E +  +  VT+NR KALNALN   + EL   +      D +  +++TG+ EK
Sbjct: 1   MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60

Query: 60  AFAAGADIGMMSTYTYMDVYKGDYITRN-----WETVRSIRKPIIAAVAGFALGGGCELA 114
           AF AGADI   S Y+     +G+ + +      +  + +  KP IAA+ GFALGGG ELA
Sbjct: 61  AFVAGADIKEFSDYSGK---QGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELA 117

Query: 115 MMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERA 174
           M C I  A+D AK G PE+ LG++PG GGTQRL + V K KA+++  TA  + A +AE+ 
Sbjct: 118 MACHIRIASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKI 177

Query: 175 GLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSL 234
           GLV+ V+P A L+ +A      I +    A+    +SV  +   T   G   E   F   
Sbjct: 178 GLVNVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASINNT--NGYATEIEEFGKC 235

Query: 235 FATEDQKEGMAAFVEKRKPVF 255
           F T D KEG+ AFVEKRK +F
Sbjct: 236 FETADFKEGVTAFVEKRKAIF 256


Lambda     K      H
   0.321    0.134    0.380 

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: 176
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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: 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