GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Klebsiella michiganensis M5al

Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= metacyc::MONOMER-20632
         (478 letters)



>FitnessBrowser__Koxy:BWI76_RS03865
          Length = 488

 Score =  296 bits (759), Expect = 8e-85
 Identities = 178/475 (37%), Positives = 259/475 (54%), Gaps = 13/475 (2%)

Query: 5   LRHYIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEV 64
           + H+I G+ VA      + NP+ T +V+A+V  GG  EV+ AV AA++AFP WA+   + 
Sbjct: 4   INHWINGKNVAGSDYFHTTNPA-TGEVLAEVASGGADEVNQAVAAAKEAFPKWANLPMKE 62

Query: 65  RSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETV-RAGRIFKYFAGEALRRHGQN 123
           R+ L+ ++G  I     +I  +   + G  + +     + RA   F++FA    + +G+ 
Sbjct: 63  RARLMRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGKT 122

Query: 124 LESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATAN 183
                  +   T  Q VGV  L++PWN P     WK AP LA GNT V+K +  +P TA+
Sbjct: 123 YPVDDKMLNY-TLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTAD 181

Query: 184 VLADIMAECGAPAGVFNMLFGRGSM-GDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQA 242
            L ++  E G PAGV N++ G G+  GDAL++H DV  VSFTG    G  +   A  +  
Sbjct: 182 RLGELALEAGIPAGVLNVVQGYGATAGDALVRHHDVRAVSFTGGTATGRNIMKNAGLK-- 239

Query: 243 RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLA 302
           +  +E+GGK+P+++ +DAD+ERA+  AL   F   G+RCTA SR+ +Q  I+ +FV   A
Sbjct: 240 KYSMELGGKSPVLIFEDADIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKRFA 299

Query: 303 EKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNP---- 358
           E+   LRVGD  DPNTQ+G  +S+   E    YI +   EG  ++ GG     D P    
Sbjct: 300 ERANRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAHLR 359

Query: 359 -GWYVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSL 417
            G ++RPT++AD    MR+  EE+FGPVA  +  K   E L +AN VE+GL++ I T  +
Sbjct: 360 NGNFLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQDV 419

Query: 418 KHARHFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTK 472
                  R   AGM  VN      D   PFGG K+S  G RE G  + E F + K
Sbjct: 420 SKVLRLARGIEAGMVFVNTQNVR-DLRQPFGGVKASGTG-REGGEYSFEVFAEMK 472


Lambda     K      H
   0.317    0.133    0.384 

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: 576
Number of extensions: 26
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: 478
Length of database: 488
Length adjustment: 34
Effective length of query: 444
Effective length of database: 454
Effective search space:   201576
Effective search space used:   201576
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