GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Sinorhizobium meliloti 1021

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Smeli:SMc04397
          Length = 504

 Score =  358 bits (920), Expect = e-103
 Identities = 189/471 (40%), Positives = 288/471 (61%), Gaps = 15/471 (3%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANER 73
           IDG++V   +G+T + + P     +        A+ + A+ AA++A + GPW +MTA+ER
Sbjct: 24  IDGQWVDGAEGRTIERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPRMTASER 83

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTW-----LSGSIDIPRAAYNFHFFSDYIRTI 128
             +L +  D+I  R +EL+ L+++++GKP       L+G+ DI R A      +   R +
Sbjct: 84  SLILLRAADMIAARADELAFLDAVESGKPISQAKGELAGAADIWRYA------AALAREL 137

Query: 129 TNEA-TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187
           + E+   + +  L   +R P+GV+ +I PWN P L+++ KL  ALAAG T V+KP+ELT 
Sbjct: 138 SGESYNTLGEGTLGVVLREPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTS 197

Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247
            +  VL EI   AGVP GVVN++ G GP  AGA LT HP V+ +SFTG T  G++ MA+A
Sbjct: 198 ASTLVLGEILEAAGVPQGVVNIIVGTGPE-AGAPLTTHPHVDMVSFTGSTGIGQLTMANA 256

Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307
           A+TLK++S ELGGKNP ++F D+NLDE I+  +  ++ N GE C  GSR+ + R   E  
Sbjct: 257 AQTLKKVSLELGGKNPQIVFPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRDIAEEV 316

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLE 367
             +  + + ++ VGDP D +T+VGA+I+ +H +++ GY+  A  EG  I  GG   + L 
Sbjct: 317 TARIASLSAKVKVGDPLDPETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTTLD-LG 375

Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427
            G F+ PTI++ +  +  V +EE+FGPV++V+ F+  EE +   N   YGLSA VW+ D 
Sbjct: 376 MGQFMAPTILSAVRPEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVWSRDF 435

Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
                +  ++ AG VW+NT+       PFGG +QSG+GRE G H+ E Y+E
Sbjct: 436 DTCLTIGRRVRAGTVWMNTFMDGASELPFGGYRQSGLGRELGRHAVEDYTE 486


Lambda     K      H
   0.318    0.136    0.404 

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: 637
Number of extensions: 28
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: 486
Length of database: 504
Length adjustment: 34
Effective length of query: 452
Effective length of database: 470
Effective search space:   212440
Effective search space used:   212440
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: 52 (24.6 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