GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Sphingomonas koreensis DSMZ 15582

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ga0059261_2631 Ga0059261_2631 FAD/FMN-containing dehydrogenases

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__Korea:Ga0059261_2631
          Length = 493

 Score =  229 bits (585), Expect = 1e-64
 Identities = 141/460 (30%), Positives = 241/460 (52%), Gaps = 11/460 (2%)

Query: 8   ASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEH 67
           A  +AA++ ++P E V    E    +  D L +    P +++   + E+V+ ++++ +E+
Sbjct: 13  AEIVAAMRAIVPGEGVIDALEALRPYESDALTAYAQVPLLVVLPETVEQVAAVLRWCHEN 72

Query: 68  NIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVE 127
            + VV RG+GT L G  +PL  G++L     N +L++D  +    V+PGV  + +++ VE
Sbjct: 73  RVKVVPRGAGTSLSGGALPLADGVLLGMARFNRVLDIDYADRVAVVQPGVTNLAITRAVE 132

Query: 128 ENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKI 186
           +   +Y PDP  + A TI GN++ N+GG+  +KYG+T + V G+ +V   GE++ LGG+ 
Sbjct: 133 DAGFYYAPDPSSQIACTIGGNVAENSGGVHCLKYGLTTNNVLGVELVTIEGEVVRLGGRG 192

Query: 187 VKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS 246
           ++  +G  L  +++GSEG L V+T+  +++LP P+   +LLI F ++  A   V +II +
Sbjct: 193 LE-PAGLDLLGVIVGSEGLLGVVTEVTVRILPRPETAKALLIGFPDVESAGVCVAQIIAA 251

Query: 247 KAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKE--QVEAEYETVANLC 304
             IP  +E M++  I  AE F+   +P     A +++  DG   E   +  E E +A   
Sbjct: 252 GIIPAGMEMMDKPAINAAEAFVNAGYP-LDVEALLIVELDGPGAECGHLTGEVEAIAR-- 308

Query: 305 LAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDL 364
            A GA  V        +   W+ R A   A    + +    D  +PR R+ E +     L
Sbjct: 309 -AHGAVSVQASRDDAERALFWAGRKAAFPAAGRISPDYYCMDGTIPRRRLPEVLTRMKAL 367

Query: 365 AKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAK-ALTFEGLVSGEH 423
           +++  + + +  HAGDGNLH  +  D       + + AEA      K  +   G+++GEH
Sbjct: 368 SEQYGLGVINVFHAGDGNLHPLILYD--ANQPGQLERAEAFGADILKLCVEVGGVLTGEH 425

Query: 424 GIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           G+G  KR  +   F    LA    +K  FDP+ LLNP K+
Sbjct: 426 GVGVEKRDLMHTMFSETDLAQQQRVKCAFDPELLLNPGKM 465


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: 531
Number of extensions: 32
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: 493
Length adjustment: 34
Effective length of query: 432
Effective length of database: 459
Effective search space:   198288
Effective search space used:   198288
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