GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03233
          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 (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