GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Klebsiella michiganensis M5al

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Koxy:BWI76_RS03865
          Length = 488

 Score =  350 bits (898), Expect = e-101
 Identities = 199/481 (41%), Positives = 277/481 (57%), Gaps = 15/481 (3%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +ING+  +    + F   +P  G  LA+VAS    + N+AV  A+  F    W+ L P K
Sbjct: 7   WINGK--NVAGSDYFHTTNPATGEVLAEVASGGADEVNQAVAAAKEAFPK--WANL-PMK 61

Query: 83  RKAKLIR-FADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141
            +A+L+R   DL+ +NV E+A +ET D G PI  + ++ IP A+    + AE   ++  +
Sbjct: 62  ERARLMRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGK 121

Query: 142 VAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201
             P     L     +PVGV   + PWN P + A WK+ P LA GN+ VLK SE SPLTA 
Sbjct: 122 TYPVDDKMLNYTLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTAD 181

Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261
           R+ +LA+EAGIPAGVLNV+ GYG T G AL  H DV  + FTG T   + +M  AG   +
Sbjct: 182 RLGELALEAGIPAGVLNVVQGYGATAGDALVRHHDVRAVSFTGGTATGRNIMKNAG---L 238

Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321
           K+  +E GGKSP ++F DA D++ A +AA   I    GE CTAGSR+ +++SI  +F+  
Sbjct: 239 KKYSMELGGKSPVLIFEDA-DIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKR 297

Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE---- 377
             E     + G+P DP T VGAL+  Q    V  YI  G ++GA LLAGG     +    
Sbjct: 298 FAERANRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAH 357

Query: 378 -TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436
              G ++ PT+   V N MR+AQEEIFGPV  ++ F    E + +AND  YGLA+ IWT 
Sbjct: 358 LRNGNFLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQ 417

Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496
           D+SK  + AR + AG V+VN  +  D+  PFGG K SG GR+   ++ E + E+K   I 
Sbjct: 418 DVSKVLRLARGIEAGMVFVNTQNVRDLRQPFGGVKASGTGREGGEYSFEVFAEMKNVCIS 477

Query: 497 L 497
           +
Sbjct: 478 M 478


Lambda     K      H
   0.316    0.132    0.390 

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: 623
Number of extensions: 33
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: 497
Length of database: 488
Length adjustment: 34
Effective length of query: 463
Effective length of database: 454
Effective search space:   210202
Effective search space used:   210202
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: 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