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 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__Dino:3608683
          Length = 472

 Score =  159 bits (403), Expect = 1e-43
 Identities = 143/469 (30%), Positives = 214/469 (45%), Gaps = 17/469 (3%)

Query: 6   VEASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAY 65
           V A    A++  +P E  F   E+   +  +  G       +L+   +TEEV+ +++ A 
Sbjct: 5   VPADFETAVRAALP-EAAF--PELSAAYLEEPRGRYAGSGGLLVAPGATEEVATLVRLAQ 61

Query: 66  EHNIPVVVRGSGTGLVGACVPLFGGI--MLETTLMNNILELDTENLTVTVEPGVLLMELS 123
            H +P++  G GTGLVG  +   G +  +L    M +I  +  E   +  + G +L E+ 
Sbjct: 62  AHKVPIIPYGGGTGLVGGQIAPAGPVPVILSLRRMRSIRAVYPEENVLVADAGAVLAEVQ 121

Query: 124 KFVEENDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIEL 182
           +   +    +P     E SATI G ++TNAGG+  ++YG  RD   GL  V+ +G I   
Sbjct: 122 QAARDVGRLFPLSLASEGSATIGGVLATNAGGVNVLRYGNARDLCLGLEAVMPDGAIWHG 181

Query: 183 GGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPK 242
             ++ KN+ GY L+ L+IG+EGTL +IT A L+L PLP+     L+  +  S AA +   
Sbjct: 182 LTRLRKNNMGYDLRHLLIGAEGTLGIITGAALRLSPLPQRHGVGLLVVD--SPAAALDLL 239

Query: 243 IIKSKAIPTAIEFME----RQTILFAEDFLGKKFPDSSSNAY-ILLTFDGNTKEQVEAEY 297
            +  +     I   E    R    FAE     + P     A+ +L+   G +    E   
Sbjct: 240 ALAGEVAGDTISAFELISGRGFEFFAETMPEMRAPLDPVPAWSVLIDLAGASGFDPEGAL 299

Query: 298 ETV-ANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAE 356
           ET+ A    A    D  I  +  + D++W+ R    EA       +   D+ VP + I  
Sbjct: 300 ETLFARAAEAGLVSDGVIAQSEAQADALWALRENIPEA-NRRIGSVSSHDISVPLSEIPN 358

Query: 357 FIE-FTHDLAKEMDVRIPSFGHAGDGNLHIYVC-RDELCQADWEAKLAEAMDRMYAKALT 414
           FIE  T  LA   D RI  FGH GDGNLH  V  +    +AD E +       ++     
Sbjct: 359 FIETATARLAGIGDYRINCFGHVGDGNLHYNVFPQPGRSRADHEDERPAIKTCVHDLVHE 418

Query: 415 FEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
             G VS EHG+G  K + L         A M  IK   DP  L+NP  V
Sbjct: 419 LGGSVSAEHGVGRLKVEDLERYGDPVKQAAMRAIKDALDPHGLMNPGAV 467


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: 495
Number of extensions: 20
Number of successful extensions: 6
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: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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