GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Desulfoscipio geothermicus DSM 3669

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_900115975.1:WP_092482996.1
          Length = 396

 Score =  240 bits (613), Expect = 5e-68
 Identities = 146/410 (35%), Positives = 221/410 (53%), Gaps = 50/410 (12%)

Query: 42  RGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAII 101
           RGEG R++D DG  F DF  G+ V ++GH HP VV AI++QA +  H S   ++ E    
Sbjct: 27  RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNL-YYIEPQAR 85

Query: 102 LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK------YGTGRKQFLAFYHAFHGRT 155
           LAE L++ +  D   +V + NSGAEANE A+KL +      +G  + + +    +FHGRT
Sbjct: 86  LAELLVQNSCCD---RVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGRT 142

Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215
            A ++ T     QQ GF P  PG  ++P+ +P                     D +E   
Sbjct: 143 LAAITATGQPKYQQ-GFEPLPPGFKYVPFNDP---------------------DALE--- 177

Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275
            R + PH   A+  EP+QGEGG       +   +++  D  G+LL  DEVQ G+GRTG+F
Sbjct: 178 -RAIGPHTC-AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEF 235

Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAAGIEV 334
            A +H+ VEPD+I   KA+GGG P+  ++ +  +     PG HATTFGGNP+A AAG+  
Sbjct: 236 LAYQHYDVEPDIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAA 295

Query: 335 VEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE 392
           ++ +    ++ + + VG Y  + L++   KY+ I + RGLGL   +E+ +          
Sbjct: 296 MQTMLGDGVMQNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRP--------- 346

Query: 393 LRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKA 442
               IV    ++GL++    +N +RF PPL++  EE+D A+E  E  L A
Sbjct: 347 -GGDIVNRCREKGLLINCVNNNVLRFTPPLVIGTEEVDRALETVEAVLIA 395


Lambda     K      H
   0.320    0.141    0.418 

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: 27
Number of successful extensions: 8
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: 445
Length of database: 396
Length adjustment: 32
Effective length of query: 413
Effective length of database: 364
Effective search space:   150332
Effective search space used:   150332
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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