GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Bacillus altitudinis 41KF2b

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_035391821.1 BA79_RS18270 glycolate oxidase subunit GlcD

Query= BRENDA::H6LBS1
         (466 letters)



>NCBI__GCF_000691145.1:WP_035391821.1
          Length = 469

 Score =  328 bits (842), Expect = 2e-94
 Identities = 181/452 (40%), Positives = 270/452 (59%), Gaps = 6/452 (1%)

Query: 14  IKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVV 73
           +KE++ A  V         +S+D   +    P+ +++  + EEV +I+K    + +P+V 
Sbjct: 10  LKEIVGAPNVQDSKADRLAYSYDATPNFQQMPDAIVRPHTAEEVQQIVKLCASYKVPIVP 69

Query: 74  RGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFY 133
           RGSGT L     P  GG+++  T MN +LE+D ENLT TV+PG++  EL   VEE  LFY
Sbjct: 70  RGSGTNLCAGTCPTQGGLVILFTRMNQLLEIDEENLTATVQPGLITQELIHQVEEKGLFY 129

Query: 134 PPDPGE-KSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSG 192
           PPDP   K +T+ GNI+ N+GG+R +KYGVTRDYV GL VVL NG+II+ GGK+ K+ +G
Sbjct: 130 PPDPSSMKISTLGGNINENSGGLRGLKYGVTRDYVLGLEVVLPNGDIIKTGGKLAKDVAG 189

Query: 193 YSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTA 252
           Y +  L +GSEGTL ++T+A+LKLLPLP+   ++L  +E++ +AA  V  II  + IP  
Sbjct: 190 YDMTRLFVGSEGTLGIVTEAVLKLLPLPETKQTMLCLYESLEEAATSVSAIIAERIIPAT 249

Query: 253 IEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDV 312
           +EFM++ T+   EDF     P +   A +L+  DGN  E V  + + +A +C   GA  V
Sbjct: 250 LEFMDQPTLEVVEDFANIGLP-TDVQAVLLIEQDGN-PEAVSRDIQKIAEVCEQHGATSV 307

Query: 313 YIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVR 371
            I  + E   ++ +AR + L A+ + S T + E D  VPR+ IA  +    D+A++ +V 
Sbjct: 308 KIAHSEEEASALLTARRSALSALARLSPTTILE-DATVPRSEIANMVRAIEDIARKYEVN 366

Query: 372 IPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRK 431
           I +FGHAGDGNLH   C  +    +   ++  A   ++ KA+   G ++GEHG+G  K  
Sbjct: 367 ICTFGHAGDGNLH-PTCATDARNEEEMKRVEAAFQAIFEKAVALGGTITGEHGVGLMKAP 425

Query: 432 YLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           YL      E +A M  IKQ  DP +++NP KV
Sbjct: 426 YLELKVKKEGIAAMKAIKQALDPAHIMNPDKV 457


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: 492
Number of extensions: 24
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 24 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