GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Azospirillum brasilense Sp245

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase

Query= curated2:C3P3K3
         (396 letters)



>FitnessBrowser__azobra:AZOBR_RS19025
          Length = 389

 Score =  243 bits (619), Expect = 9e-69
 Identities = 139/372 (37%), Positives = 206/372 (55%), Gaps = 6/372 (1%)

Query: 19  YHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA 78
           Y    IV  + EG ++   +G R++D  +  +    GH +P ++ AL  QA+++  TS  
Sbjct: 9   YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68

Query: 79  FHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCE 138
           F         +++ + T  + V   N+GAEA E   K  R++ Y+  K +  R  II  E
Sbjct: 69  FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYE--KGDKARTRIITFE 126

Query: 139 DNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGE 198
             FHGRT+ AVS +  E+  +GFGP+L G  ++P+GDLEA++ A+T  TA   LEPIQGE
Sbjct: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGE 186

Query: 199 AGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALG 258
            GI      FL+   E+C +  +L   DEIQ G+GRTGK+FA +W  +TPD+  + K +G
Sbjct: 187 GGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIG 246

Query: 259 GGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQLGEK 318
           GG FP+    A          G+HGST+GGNPLA AV  A L+ + E    +   ++G  
Sbjct: 247 GG-FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305

Query: 319 LVGQLKEI--DNPMITE-VRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIRIAP 375
           L  +L  +  +NP + + VRGKGL +G+            L+A GLL     +NV+R+ P
Sbjct: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLP 365

Query: 376 PLVISEEDLEWA 387
           PL I E ++E A
Sbjct: 366 PLNIGEAEVEEA 377


Lambda     K      H
   0.317    0.136    0.402 

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: 393
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: 396
Length of database: 389
Length adjustment: 31
Effective length of query: 365
Effective length of database: 358
Effective search space:   130670
Effective search space used:   130670
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: 50 (23.9 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