GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Pseudomonas fluorescens FW300-N2E3

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AO353_08505 AO353_08505 FAD-linked oxidase

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_08505 AO353_08505 FAD-linked
           oxidase
          Length = 464

 Score =  215 bits (548), Expect = 2e-60
 Identities = 141/462 (30%), Positives = 234/462 (50%), Gaps = 16/462 (3%)

Query: 11  IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70
           I  +K L+   +V    +    +  D        P  ++   +TE+V  I+++A EH I 
Sbjct: 7   IEELKTLVEPGKVLTDADSLNAYGKDWTKHFAPAPTAIVFPKTTEQVQAIVRWANEHKIA 66

Query: 71  VVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130
           +V  G  TGL  A V   G +++    MN IL+++  + T   +PGV+  +L    EE+ 
Sbjct: 67  LVPSGGRTGLSAAAVAANGEVVVSFDYMNQILDVNLTDRTAVCQPGVVTEQLQNRAEEHG 126

Query: 131 LFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189
           L+YP D     S+ I GNI TNAGG++ ++YG+TR++V G+ VV   G+++EL   ++KN
Sbjct: 127 LYYPVDFASAGSSQIGGNIGTNAGGIKVIRYGMTRNWVAGMKVVTGKGDLLELNRDLIKN 186

Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKI--IKSK 247
           ++GY L+ L IG+EGTL  + +A ++L   PK   ++++     +D   I+P +   +SK
Sbjct: 187 ATGYDLRQLFIGAEGTLGFVVEATMRLDRAPKNLTAMVL---GTADFDSIMPVLHAFQSK 243

Query: 248 AIPTAIEFMERQTI--LFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCL 305
              TA EF   + +  + A   +   F +S    Y LL F+  T+E      ET  + C+
Sbjct: 244 LDLTAFEFFSDKALAKVLARGDVPAPF-ESDCPFYALLEFEATTEEVANHALETFEH-CV 301

Query: 306 AEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDL 364
            EG   D  +  +  +  ++W  R    E I   T   ++  V V  +++  F++    +
Sbjct: 302 EEGWVLDGVMSQSESQLQNLWKLREYISETISHWTPYKNDISVTV--SKVPAFLKEVDAI 359

Query: 365 AKE--MDVRIPSFGHAGDGNLHIYVCRDE-LCQADWEAKLAEAMDRMYAKALTFEGLVSG 421
             E   D  I  FGH GDGNLH+ + + E L + ++ AK A     ++     + G +S 
Sbjct: 360 VGEHYPDFEIVWFGHIGDGNLHLNILKPENLSKDEFFAKCATVNKWVFETVEKYNGSISA 419

Query: 422 EHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           EHG+G  KR YL        +  M  +K  FDP  ++NP K+
Sbjct: 420 EHGVGMTKRDYLTYSRSPVEIEYMKAVKAVFDPNGIMNPGKI 461


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: 529
Number of extensions: 25
Number of successful extensions: 5
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: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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