GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas fluorescens GW456-L13

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate PfGW456L13_1795 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1795
          Length = 482

 Score =  232 bits (592), Expect = 2e-65
 Identities = 153/479 (31%), Positives = 245/479 (51%), Gaps = 11/479 (2%)

Query: 8   GHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLR 67
           G YI+G+  A  N  L  V NPAT A+   V   +   VD AV++A  AF  WS+ S   
Sbjct: 9   GLYINGQWSAG-NEHL-RVINPATEALLTTVNGGDERAVDQAVSAATQAFADWSKTSGAE 66

Query: 68  RSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFS 127
           R  ++ K    +  + ++L  + S  +GK   +A  +V   I   EY  G    L     
Sbjct: 67  RGAILRKIATGVQANREKLMHLQSSNNGKPQFEAAIDVDDVIATFEYYAGLAEGLDAKQD 126

Query: 128 DNIGGGIDNWNLR---QPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSA 184
             +    D+++ R   +P GV   + P+NFP++   W +  AL AG C +LKPSE  P  
Sbjct: 127 SAVELPTDDFSARLRREPCGVVGLIVPWNFPMVTTAWKLAPALAAGCCVVLKPSEVTPLP 186

Query: 185 SLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQ-HPDIEAISFVGSTPIAEYIHQQGTAQ 243
            L +A ++ EAG+P GVFN+V G  +AV A L   P I  +SF GS  +   + Q+    
Sbjct: 187 ELELAAIIAEAGVPAGVFNLVCGTGLAVGAPLSADPRIAKVSFTGSNAVGVQVMQRAAET 246

Query: 244 GKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAK 303
            K V    G K+ ++V+ DAD + A +   G  + +AG+ C A S  +   ++ DE + +
Sbjct: 247 VKGVSLELGGKSSLLVLADADPELAVEVACGGGFFNAGQMCSATSRVLVADELADEFLNR 306

Query: 304 LLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQ 363
           +  R + +++ +   P  +MG LV      +V G ID G++ GA+L+  G   +     +
Sbjct: 307 VKARAEAIRVADPFDPNVEMGALVNQAQYQRVLGHIDRGLSAGAKLVCGGN--RPADLPR 364

Query: 364 GFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGG 423
           G+F+  T+F +V  + +++ +EIFGPV+ + R    A A+AL N  +FG   S  TR+  
Sbjct: 365 GYFLQPTVFTEVPLDSALWNEEIFGPVICVRRFASEAEAIALANDSQFGLVASVVTRNAQ 424

Query: 424 IARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQ 482
            A   A +++ G+V IN P  V     ++GG+K+S  G     G  GL+ +   K V++
Sbjct: 425 TADRVANALQAGLVWINAP-QVIFPQTAWGGYKQSSIG--RELGPWGLQAFQEIKHVIR 480


Lambda     K      H
   0.320    0.137    0.412 

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: 523
Number of extensions: 29
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: 500
Length of database: 482
Length adjustment: 34
Effective length of query: 466
Effective length of database: 448
Effective search space:   208768
Effective search space used:   208768
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 (21.8 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