GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Sinorhizobium meliloti 1021

Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate SMc00832 SMc00832 glycolate oxidase subunit protein

Query= BRENDA::O29853
         (443 letters)



>lcl|FitnessBrowser__Smeli:SMc00832 SMc00832 glycolate oxidase
           subunit protein
          Length = 479

 Score =  216 bits (550), Expect = 1e-60
 Identities = 147/435 (33%), Positives = 231/435 (53%), Gaps = 28/435 (6%)

Query: 24  ETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIV 83
           ET   +A R      VV P  +E V+A+LK+ +   IP+  RG GT LSGGA+P E+ IV
Sbjct: 45  ETDAFIAYRRMP-LAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIV 103

Query: 84  LSTEKMTE-LEVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATN 141
           +   KM+  L++D  NR A   AGVT   + DA    G  + P P ++ A T+GG I  N
Sbjct: 104 VGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMN 163

Query: 142 AGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITK 201
           +GG   LKYG   N +L ++ VL DG +I +GGK + ++ GY LL L+ GSEG L ++T+
Sbjct: 164 SGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGKAL-DAPGYDLLGLVCGSEGQLGIVTE 222

Query: 202 ATIRLFPQMRDMTVLAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGER 260
           AT+RL  +      +   F + E A +CV + +   ++P+A+EFM++ A+EI E  + + 
Sbjct: 223 ATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFA-QA 281

Query: 261 WVSREGEAHLLMVFESFDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRK 320
               + EA L++  E   EAE  A +A  +     +   T ++    L+   +I++G RK
Sbjct: 282 GYPLDVEALLIVEVEG-SEAEMDATLAGIIEIARRHGVMTIRESQSALEA-ALIWKG-RK 338

Query: 321 EVIEV---------LDACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLVY 371
                         +D  VP ++++   RR+ E+   YG+ +    HAGDGN+  HPL+ 
Sbjct: 339 SAFGATGRIADYICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNM--HPLIL 396

Query: 372 EGWEKSYFEFR-----KSLLSLAVSLGGVISGEHGIGAVKLSELEELFPEQFELMRQI-- 424
                     R       +L L V  GG ++GEHG+G  K   +   +  + +L +Q+  
Sbjct: 397 YNINDPEEAARAEAAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQY-SRADLGQQMAA 455

Query: 425 KLLFDPKNILNPGKV 439
           +  FDP+ ++NP KV
Sbjct: 456 RAAFDPQWLMNPSKV 470


Lambda     K      H
   0.317    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: 488
Number of extensions: 28
Number of successful extensions: 7
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: 443
Length of database: 479
Length adjustment: 33
Effective length of query: 410
Effective length of database: 446
Effective search space:   182860
Effective search space used:   182860
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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