GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Dinoroseobacter shibae DFL-12

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 3609512 Dshi_2896 FAD linked oxidase domain protein (RefSeq)

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__Dino:3609512
          Length = 480

 Score =  223 bits (569), Expect = 8e-63
 Identities = 139/455 (30%), Positives = 235/455 (51%), Gaps = 9/455 (1%)

Query: 11  IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70
           +A ++E++P + V         +  D L +    P   +  +STEEV+ ++K  +   +P
Sbjct: 18  VALLQEVLPRDAVIHEPHETRAYECDALTAYKCPPLAAVLPSSTEEVAAVLKICHAEGVP 77

Query: 71  VVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130
           VV RGSGT L G  +P    ++L    +N +LE D +N  + V+ G   + +S  VEE D
Sbjct: 78  VVPRGSGTSLAGGALPTADCVILGVARLNKVLETDYDNRIIRVQSGRTNLSVSGAVEEED 137

Query: 131 LFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189
            FY PDP  + A  IAGNI+ N+GG   +KYGVT + + G+T+V+ +G ++ +GG  + +
Sbjct: 138 FFYAPDPSSQLACAIAGNIAMNSGGAHCLKYGVTTNNLLGVTMVMMDGTVVTIGGAHL-D 196

Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAI 249
           + G  L  ++ GSEG L V+T+A L++L  P+    +LI F+    A   V  IIK+  +
Sbjct: 197 AGGLDLLGVICGSEGQLGVVTEATLRILRKPEGARPVLIAFDENEVAGACVADIIKAGVL 256

Query: 250 PTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGA 309
           P AIEFM++  I   E+F    +P+    A +++  +G+  E ++A+   + ++      
Sbjct: 257 PVAIEFMDKLCIETCENFAKAGYPE--CEALLIVEVEGSEAE-IDAQLGVILDIARKHNP 313

Query: 310 KDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369
            ++    + E    +W  R +   AI      M   D  +P + +   +    +++KE  
Sbjct: 314 VELRQSQSAEESAKIWLGRKSAFGAIGQLNDYMC-LDGTIPVSELPYVLRRIGEMSKEYG 372

Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAK-ALTFEGLVSGEHGIGYA 428
           +++ +  HAGDGN+H  +  D     D + +L EA      K  +   G ++GEHG+G  
Sbjct: 373 LQVGNVFHAGDGNMHPLILFD--ANKDGDLELCEAFGAEILKLCVEVGGCLTGEHGVGIE 430

Query: 429 KRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           KR  +   F    + +   +K  FDP  LLNP KV
Sbjct: 431 KRDLMGAQFTGADMEMQLRVKDVFDPAWLLNPAKV 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: 520
Number of extensions: 29
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: 480
Length adjustment: 33
Effective length of query: 433
Effective length of database: 447
Effective search space:   193551
Effective search space used:   193551
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