GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Caulobacter crescentus NA1000

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03233 CCNA_03233 Acetyl ornithine
           aminotransferase
          Length = 467

 Score =  196 bits (497), Expect = 2e-54
 Identities = 134/427 (31%), Positives = 226/427 (52%), Gaps = 33/427 (7%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYEN 98
           ++ R +G  + D DG+   D  +G+  +NVG+    + +A  +Q  +  +Y+    F++ 
Sbjct: 39  IVTRADGCYITDGDGHRILDGMAGLWCVNVGYGRKELADAAYEQMLELPYYNT---FFKT 95

Query: 99  A----IILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFY 148
           A    + LA K+ E   G +   V + +SG+EAN+   +LV++         R  F++ +
Sbjct: 96  ATPPTVKLAAKIAEKMGGHLTH-VFFNSSGSEANDTVFRLVRHYWKLKGQPNRTVFISRW 154

Query: 149 HAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVL 208
           +A+HG T A +SL   K +   G  P +PGV H+  P P+   +G    E+P    +R +
Sbjct: 155 NAYHGSTVAGVSLGGMKHMHVQGDLP-IPGVEHVMQPYPFGEGFG----EDPAAFRDRAV 209

Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268
             IE+ +   V P  + A   EP+QG GG ++PP G++ A++    +YGILL  DEV  G
Sbjct: 210 KEIEDKILE-VGPENVAAFIGEPVQGAGGVIIPPDGYWPAVEAVCRKYGILLVCDEVICG 268

Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV---IHRADITFDKPGR--HATTFG 322
            GR G+++  +H+G++PDLI   K +  G LP++ V    H      +K G   H  T+ 
Sbjct: 269 FGRLGQWFGHQHYGIKPDLIAMAKGLSSGYLPISAVGVADHIVAELREKGGDFIHGFTYS 328

Query: 323 GNPVAIAAGIEVVEIV--KELLPHVQE-VGDYLHKYLEEFKEKYEVIGDARGLGLAQAVE 379
           G+P   A  ++ +EI+  ++L+   +E  G YL K L    + + ++G+ R LGL  AVE
Sbjct: 329 GHPTCAAVALKNIEIIEREDLITRTREDTGPYLAKALARLND-HPLVGETRSLGLIGAVE 387

Query: 380 IVKSKETKEKYPELRDR---IVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIF 436
           IV+ K T  ++ +       IV++   R  +++    +SI   PPLIV+  EID  + I 
Sbjct: 388 IVREKGTNHRFLDKEGEAGPIVRDICIRNGLMVRAIRDSIVCCPPLIVSHAEIDELVGII 447

Query: 437 EEALKAA 443
           E++L  A
Sbjct: 448 EKSLTEA 454


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: 620
Number of extensions: 44
Number of successful extensions: 7
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: 467
Length adjustment: 33
Effective length of query: 412
Effective length of database: 434
Effective search space:   178808
Effective search space used:   178808
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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