GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_08505
          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:

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