GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Pseudomonas putida KT2440

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate PP_5154 PP_5154 putative Oxidoreductase, FAD-binding

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__Putida:PP_5154 PP_5154 putative Oxidoreductase,
           FAD-binding
          Length = 455

 Score =  199 bits (507), Expect = 1e-55
 Identities = 131/428 (30%), Positives = 216/428 (50%), Gaps = 16/428 (3%)

Query: 45  PEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILEL 104
           P  ++   + E+V  I+ +A  H + +V  G  TGL    V   G +++    MN IL  
Sbjct: 31  PSAIVFPKTIEQVQAIVHWANAHKVALVPSGGRTGLSAGAVAANGEVVVAFDYMNQILGF 90

Query: 105 DTENLTVTVEPGVLLMELSKFVEENDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVT 163
           +  + TV  +PGV+  +L  + EE  L+YP D     S+ I GNI TNAGG++ ++YG+T
Sbjct: 91  NAFDRTVVCQPGVVTRQLQTYAEEQGLYYPVDFASSGSSQIGGNIGTNAGGIKVIRYGMT 150

Query: 164 RDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMT 223
           R++V GL VV   GE++EL   ++KN++GY L+ L IG+EGTL  + +A ++L   P+  
Sbjct: 151 RNWVAGLKVVTGKGELLELNKDLIKNATGYDLRQLFIGAEGTLGFVVEATMRLDRAPRNL 210

Query: 224 LSLLIPFENISDAAGIVPKI--IKSKAIPTAIEFMERQTI--LFAEDFLGKKFPDSSSNA 279
            ++++      D   I+P +   + K   TA EF   + +  + A   +   F  +    
Sbjct: 211 TAMVL---GTPDFDSIMPVLHAFQGKLDLTAFEFFSDKGLAKILARGDVPAPFA-TDCPF 266

Query: 280 YILLTFDGNTKEQVEAEYETVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKAS 338
           Y LL F+ +T E V  E       C+ +G   D  +  +  +  ++W  R    E I   
Sbjct: 267 YALLEFEAST-EDVANEALATFEHCVEQGWVLDGVMSQSESQLKNLWKLREYLSETISHW 325

Query: 339 TTEMDECDVVVPRNRIAEFIEFTHDLAKE--MDVRIPSFGHAGDGNLHIYVCRDE-LCQA 395
           T   ++  V V  +++  F+     +  E   D  +  +GH GDGNLH+ + + E + + 
Sbjct: 326 TPYKNDISVTV--SKVPAFLRDIDAIVSEHYPDYEVVWYGHIGDGNLHLNILKPEHMSKD 383

Query: 396 DWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPK 455
           D+ A  A+    ++     + G +S EHG+G  KR YL      E +A M  IK  FDP 
Sbjct: 384 DFFASCAKVNKWVFEIVERYNGSISAEHGVGMTKRDYLGYSRSPEEIACMKAIKAVFDPN 443

Query: 456 NLLNPKKV 463
            ++NP K+
Sbjct: 444 GIMNPGKI 451


Lambda     K      H
   0.318    0.136    0.388 

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: 507
Number of extensions: 27
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: 466
Length of database: 455
Length adjustment: 33
Effective length of query: 433
Effective length of database: 422
Effective search space:   182726
Effective search space used:   182726
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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