GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Pseudomonas putida KT2440

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__Putida:PP_2694 PP_2694 Aldehyde dehydrogenase
           family protein
          Length = 480

 Score =  255 bits (651), Expect = 3e-72
 Identities = 156/475 (32%), Positives = 245/475 (51%), Gaps = 6/475 (1%)

Query: 9   NYINGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67
           NYI+G+W E          +P+ T +++ Q   ++ E    A Q A  A   W+   +  
Sbjct: 8   NYIDGQWCEGHATLGN--YSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGLES 65

Query: 68  RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127
           R ++L      L   KEEL  L++ E GK   E +GEV R  +   + A      MG++ 
Sbjct: 66  RQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGETA 125

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
           AS+   V+   +R P+GVVG I P+NFPM    W    A+A GN  + KP+   P     
Sbjct: 126 ASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASAWA 185

Query: 188 LVELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246
           L E+  + GLP G FN+V G+  DV   +++  EI A++F GS   G  V    + NL R
Sbjct: 186 LTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATAGNLVR 245

Query: 247 VQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQE 306
            Q   G+KN  +V++DA+LE  V   +  AF   G++C A + + V +GI D F+  L+ 
Sbjct: 246 CQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHDRFVEALRL 305

Query: 307 KVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVG 365
           ++  +K+G+ L+ GV +GPV      ++ L+Y++    EGA L+  G R  ++ DGY++ 
Sbjct: 306 RMRQLKVGHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQLACDGYYMR 365

Query: 366 PTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYF 425
           P +F N   +M I ++E+F P+  VIRV++ +EA+   N +E+   A + T +     +F
Sbjct: 366 PALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIITQSLRHASHF 425

Query: 426 RENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480
           +     G + +NL         PF G K+S FG     G+ + DFYT  K    R
Sbjct: 426 KRRAQTGCVMVNLPTAGTDYHVPFGGRKASSFGP-REQGQYARDFYTVVKTTYLR 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: 541
Number of extensions: 19
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: 487
Length of database: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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