GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Herbaspirillum seropedicae SmR1

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate HSERO_RS23440 HSERO_RS23440 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__HerbieS:HSERO_RS23440
          Length = 394

 Score =  159 bits (402), Expect = 1e-43
 Identities = 117/381 (30%), Positives = 179/381 (46%), Gaps = 27/381 (7%)

Query: 61  AIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSITANA 119
           A+R+ V      E+AP   E     +FP  +  KLG +GV G ++ + YG  GL   A+ 
Sbjct: 17  ALREAVAAFAHSEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVSEEYGGAGLGYLAHI 76

Query: 120 IATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDN 179
           IA  EI+R  AS       HS+L +  I   G+E QK KYLP L   + +   A++EP+ 
Sbjct: 77  IAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPRLISGDFIGALAMSEPNA 136

Query: 180 GSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQING---FIVKKDA 236
           GSD   +   A K    + +NG K WI N   AD+L+++A+        G   F+V+K  
Sbjct: 137 GSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLEAGARGMTAFLVEKGY 196

Query: 237 PGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRVMVAWQP 295
            G    +  +K+G+R    G+++ Q+  VP+E+ L GV          L   R +++  P
Sbjct: 197 KGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLDFERSVLSGGP 256

Query: 296 IGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK--LYET 353
           +GI     D+   Y+ +RKQFG  +  FQL Q KL  M   + A        CK  +Y  
Sbjct: 257 LGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMA--------CKAYVYAV 308

Query: 354 GQMTPGQASLGKA------------WISSKARETASLGRELLGGNGILADFLVAKAFCDL 401
           GQ      S  K             + + KA   A    + LGGNG + ++ V + + D 
Sbjct: 309 GQACDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWRDA 368

Query: 402 EPIYTYEGTYDINTLVTGREV 422
           +      GT +I  ++ GRE+
Sbjct: 369 KLYEIGAGTSEIRRMLIGREL 389


Lambda     K      H
   0.319    0.133    0.399 

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: 380
Number of extensions: 22
Number of successful extensions: 5
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: 436
Length of database: 394
Length adjustment: 31
Effective length of query: 405
Effective length of database: 363
Effective search space:   147015
Effective search space used:   147015
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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