GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Streptomyces kebangsaanensis SUK12

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  240 bits (612), Expect = 1e-67
 Identities = 144/441 (32%), Positives = 235/441 (53%), Gaps = 15/441 (3%)

Query: 56  NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115
           +PA  ++ V +   A  D  + A+ +A EAF  W    P +R++ L + A ++  R  +F
Sbjct: 42  DPATGEE-VHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDF 100

Query: 116 SAWLVHEAGKPWK-EADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYT-PMG 173
           +     + GKP K   + D    ID   ++A     L +G+      G+   Y    P+G
Sbjct: 101 ARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHL-QGQSAGEYSGDHTSYVRREPIG 159

Query: 174 VTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINY 233
           V  +I+PWN+ L +     +  I  GNT+VLKPA  TP+ +  F +   +AG+P GVIN 
Sbjct: 160 VVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINI 219

Query: 234 VPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTV 293
           V G+G E G++LV HP  ++++FTGS  VG R+ E A         +KR+ +E+GGK   
Sbjct: 220 VTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATA------SVKRLHLELGGKAPF 273

Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353
           VV  DADL+ A    +  A   +GQ C+A +RA + + +Y+E + +T AL + + +GDP 
Sbjct: 274 VVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPF 333

Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGGE---GDSSTGFFIQPTIIADLDPEA 410
                +GP+I     +++  +++  +   R++TGGE   G+   G + +PT+IA    ++
Sbjct: 334 APGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAPQGELKNGAYYRPTLIAGAAQDS 393

Query: 411 VIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYF 470
            I+Q EIFGPV+     +  D  + +AN+T YGL  +  +R+     +A RE   G ++ 
Sbjct: 394 EIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWV 453

Query: 471 NRNCTGAIVGYHPFGGFKMSG 491
           N +    I+   P GG K SG
Sbjct: 454 NDHI--PIISEMPHGGSKQSG 472


Lambda     K      H
   0.316    0.134    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: 670
Number of extensions: 28
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: 515
Length of database: 511
Length adjustment: 35
Effective length of query: 480
Effective length of database: 476
Effective search space:   228480
Effective search space used:   228480
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 (21.6 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