GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Klebsiella michiganensis M5al

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Koxy:BWI76_RS10695
          Length = 495

 Score =  237 bits (604), Expect = 8e-67
 Identities = 156/462 (33%), Positives = 244/462 (52%), Gaps = 14/462 (3%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAVPR 67
           +INGE+  +  +     ++PA ++ L +V    K D+D A Q A   F    WS+ +  +
Sbjct: 23  FINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVDRAVQAARGVFDRGDWSQASPAQ 82

Query: 68  RARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDS 126
           R  +L  F  L+  H+EELA L T++ GK  + +L  ++      + + A A   + G+ 
Sbjct: 83  RKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE- 141

Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186
           +A    +  A   R PIGV+  + P+NFP+++ CW    A+A GN+ +LKPSE++PL   
Sbjct: 142 VAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGPALASGNSVVLKPSEKSPLTAL 201

Query: 187 KLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYK-KGSENL 244
           +L  L ++AGLP GVFNVV G  H+    +  HP+++ I+F GS    + + K  G  N+
Sbjct: 202 RLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVITFTGSTRTAKQLLKDAGDSNM 261

Query: 245 KRVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAK 303
           KRV    G K+  IV  D  +L+  V    G  F + G+ C+A   + +EE IAD F+  
Sbjct: 262 KRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQVCIAGTRLLLEESIADRFLDL 321

Query: 304 LQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYF 363
           L+E+    + GN LD    +G +I   +     S+I  G E  + L+ DGR+N       
Sbjct: 322 LKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAG-EAHSTLLLDGRKNPWPAA-- 378

Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423
           VGPTIF +V     + ++EIF PVL V R KN ++A+ +AN S +  GA ++T + +   
Sbjct: 379 VGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALANDSRYGLGAAVWTRDLSRAH 438

Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG---TLHA 462
                + AG + +N      M   PF G+K S  G   +LHA
Sbjct: 439 RVSRRLKAGSVFVNNYNDGDMT-VPFGGYKQSGNGRDKSLHA 479


Lambda     K      H
   0.318    0.136    0.396 

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: 509
Number of extensions: 32
Number of successful extensions: 7
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: 487
Length of database: 495
Length adjustment: 34
Effective length of query: 453
Effective length of database: 461
Effective search space:   208833
Effective search space used:   208833
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