GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas stutzeri RCH2

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__psRCH2:GFF4212
          Length = 452

 Score =  198 bits (503), Expect = 3e-55
 Identities = 126/411 (30%), Positives = 230/411 (55%), Gaps = 30/411 (7%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF--- 95
           +I +  G+ ++D +G+   D  +G+  +N+G+    +VEA  +Q  +  +Y+L  FF   
Sbjct: 34  IITKASGVYLWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNL--FFQTA 91

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFYH 149
           +  A+ LA+ + ++AP  +   V +  SG+EAN+  +++V++         +K  +  ++
Sbjct: 92  HPPAVALAKAIADIAPAGMNH-VFFTGSGSEANDTVLRMVRHYWAIKGQPAKKVVIGRWN 150

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
            +HG T A  SL   K + +    P +PG+ HI  P  +    G  G   P+E   R+ D
Sbjct: 151 GYHGSTIAGASLGGMKAMHEQSDGP-IPGIEHIDQPYWF----GEGGDMSPEEFGVRIAD 205

Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269
            +E+ +   V   ++ A   EPIQG GG ++PP+ ++  +K+    Y IL   DEV  G 
Sbjct: 206 QLEQKILE-VGEDKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGF 264

Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI--TFDKPGR--HATTFGGN 324
           GRTG+++  +++G+EPDL+   K +  G +P+ GVI R ++  T ++ G   H  T+ G+
Sbjct: 265 GRTGEWFGSDYYGLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGH 324

Query: 325 PVAIAAGIEVVEIVKE--LLPHVQ-EVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIV 381
           PVA A  +E + I++E  ++  V+ +   YL    +E  + + ++G+ARG+GL  A+E+V
Sbjct: 325 PVAAAVALENIRILREEKIVERVKTKTAPYLQSRWQELLD-HPLVGEARGVGLLGALELV 383

Query: 382 KSKETKEKY--PELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEID 430
           K+K+T+E++  P +     +   + GLV+   GD  I   PPL++++E+ID
Sbjct: 384 KNKKTRERFADPGVGMLCREHCFRNGLVMRAVGDTMI-ISPPLVISEEQID 433


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: 562
Number of extensions: 40
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: 445
Length of database: 452
Length adjustment: 33
Effective length of query: 412
Effective length of database: 419
Effective search space:   172628
Effective search space used:   172628
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