GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Desulfoscipio geothermicus DSM 3669

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_900115975.1:WP_092482996.1
          Length = 396

 Score =  298 bits (764), Expect = 1e-85
 Identities = 163/384 (42%), Positives = 225/384 (58%), Gaps = 8/384 (2%)

Query: 18  HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77
           H Y  IG+   RGEG  +WD DG  +LD +   +  S GHCHP ++ A+ EQA RL   S
Sbjct: 16  HTYGRIGLAPVRGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVS 75

Query: 78  RAFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIV 137
             ++ +  A   E +   +   +V   NSGAEA E AIK  RKW  +  G   D+ EII 
Sbjct: 76  NLYYIEPQARLAELLVQNSCCDRVFFCNSGAEANEGAIKLARKWAKKQHGA--DKYEIIT 133

Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQ 197
              +FHGRTL  +  +  P+ +  F P  PGF+ +PF D  ALE+AI P+T A ++EP+Q
Sbjct: 134 AEKSFHGRTLAAITATGQPKYQQGFEPLPPGFKYVPFNDPDALERAIGPHTCAVMLEPVQ 193

Query: 198 GEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKA 257
           GE GV    + Y   VRELC  N ++LV DE+Q GLGRTG+ LA QH  +E D+  L KA
Sbjct: 194 GEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEPDIITLAKA 253

Query: 258 LAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQG 317
           L GGF P+ A+L+   V     PG H +TFGGNPLACA   AAM+ ++ +G+++N    G
Sbjct: 254 LGGGF-PIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVMQNCRAVG 312

Query: 318 ARLLEGLKDI--RANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375
           A   E L+D+  + + ++EVRG GL+L +EL+   G     C   + KG+L    + + +
Sbjct: 313 AYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPGGDIVNRC---REKGLLINCVNNNVL 369

Query: 376 RIAPPLVITSDEVDWALEQFATTL 399
           R  PPLVI ++EVD ALE     L
Sbjct: 370 RFTPPLVIGTEEVDRALETVEAVL 393


Lambda     K      H
   0.319    0.136    0.405 

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: 428
Number of extensions: 23
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: 404
Length of database: 396
Length adjustment: 31
Effective length of query: 373
Effective length of database: 365
Effective search space:   136145
Effective search space used:   136145
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 (21.8 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