GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_5154
          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:

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