GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Magnetospirillum magneticum AMB-1

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|NCBI__GCF_000009985.1:WP_043745229.1 AMB_RS18795 FAD-binding
           oxidoreductase
          Length = 469

 Score =  176 bits (445), Expect = 2e-48
 Identities = 140/431 (32%), Positives = 215/431 (49%), Gaps = 21/431 (4%)

Query: 48  LIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGG--IMLETTLMNNILELD 105
           +++  ST EV+++++      IP+V +G  TGL G  VP   G  +++ T  +  I  +D
Sbjct: 41  VVRPGSTAEVAEVVRLCAAAGIPMVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVD 100

Query: 106 TENLTVTVEPGVLLMELSKFVEENDLFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTR 164
             + T+T E G +L  L +  EE    +P   G E S  I GNISTNAGG   ++YG TR
Sbjct: 101 PVDFTLTAEAGCVLANLQQAAEEAGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTR 160

Query: 165 DYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTL 224
           D V GL VVL +G +     ++ K+++GY+L+ L IG+EGTL ++T  +LKL P P+   
Sbjct: 161 DLVLGLEVVLPDGRVWNGLKRLRKDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPR--- 217

Query: 225 SLLIPFENISDAAGIVPKIIKSKAIP----TAIEFMERQTI-LFAEDFLGKKFPDSSSNA 279
            +   F  ++D    +P   +++       TA E + R+ + L      G + P ++ + 
Sbjct: 218 EIATAFVALADLEAALPLFSRARTASGDSVTACELVPRRGLELGMRHVPGVRAPFAAFHD 277

Query: 280 Y-ILLTFDGNTKEQVEAEYETVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKA 337
           + +LL    +    +    E +      +G A D  I ++  ++   W  R A  EA K 
Sbjct: 278 WMLLLELSSSRPGGLREALEEMLGQAFEDGLAVDAVIAESDAQRADFWRIREAIPEAQKK 337

Query: 338 STTEMDECDVVVPRNRIAEFI-EFTHDLAKEM-DVRIPSFGHAGDGNLHIYVCRDELCQA 395
               +   DV V  +R+ E I   T  +   M  VR+  FGH GDGN H  + + E   A
Sbjct: 338 EGGSIKH-DVAVATSRVPEMIRRCTRAVEAAMPGVRVVPFGHLGDGNTHFNLTQPE--GA 394

Query: 396 DWEAKLA--EAMDR-MYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTF 452
           D  A LA  E M+R ++   +  EG +S EHGIG  K   L +      L LMA IK   
Sbjct: 395 DKAAFLARWEEMNRIVHDIVVEMEGSISAEHGIGRLKVDELAHYKPGVDLDLMARIKGAL 454

Query: 453 DPKNLLNPKKV 463
           DP   +NP K+
Sbjct: 455 DPLGQMNPGKI 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: 496
Number of extensions: 20
Number of successful extensions: 4
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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