GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Streptomyces kebangsaanensis SUK12

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

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



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  365 bits (938), Expect = e-105
 Identities = 190/475 (40%), Positives = 284/475 (59%), Gaps = 5/475 (1%)

Query: 10  DCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMT 69
           D   +I G+      G+T   ++PAT E++ T    G  ++D AV AA++A  G W   T
Sbjct: 20  DGAQYIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPG-WAGAT 78

Query: 70  ANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTIT 129
             +R   L +  +++ +R E+ +  ESL  GKP  L+   D+P    N  FF+   R + 
Sbjct: 79  PGDRSDALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQ 138

Query: 130 NE-ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPM 188
            + A +      +Y  R P+GV+G I PWN PL +  WK+ PA+AAGNT+V+KPAELTP+
Sbjct: 139 GQSAGEYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPL 198

Query: 189 TATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA 248
           T+ + A+   +AG+PDGV+N+V G G   AG  L  HPDV  +SFTG T  GK +   A 
Sbjct: 199 TSLLFAQAATEAGIPDGVINIVTGTG-KEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIAT 257

Query: 249 KTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFL 308
            ++KRL  ELGGK P V+F D++L+  +   +  + IN G+ C   +R YV+RP YE F+
Sbjct: 258 ASVKRLHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFV 317

Query: 309 EKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEG-LE 367
            +  A  + + +GDPF   T +G LIS  H +RV G++  A      ++TGG+ P+G L+
Sbjct: 318 ARTAALMETVRLGDPFAPGTDLGPLISHVHRDRVAGFVDRA-RAYARVVTGGEAPQGELK 376

Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427
            G +  PT+I G  +D  +V+ EIFGPV+ V+PFD+++E +   NDT YGL+AS W+ D+
Sbjct: 377 NGAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDV 436

Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482
            RA+R   +I+AG VWVN         P GG KQSG G++   +SFE Y+++ ++
Sbjct: 437 YRANRATREIKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491


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: 605
Number of extensions: 19
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: 486
Length of database: 511
Length adjustment: 34
Effective length of query: 452
Effective length of database: 477
Effective search space:   215604
Effective search space used:   215604
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 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