GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Azospirillum brasilense Sp245

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AZOBR_RS03635 AZOBR_RS03635 aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__azobra:AZOBR_RS03635
          Length = 471

 Score =  209 bits (533), Expect = 1e-58
 Identities = 145/429 (33%), Positives = 230/429 (53%), Gaps = 29/429 (6%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKF-THYSLTDFF 95
           P++IERGEG+RV+D  G  + +  + +  +++G    R+VEA  +Q  K  T++      
Sbjct: 46  PLIIERGEGVRVFDDSGKEYIEGLASLWCVSLGWGEERLVEAATRQMRKLPTYHVFGHKS 105

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG------RKQFLAFYH 149
           +E  I LAE+LI+LAP  +  KV + NSG+EAN+ A+KLV Y         +K+ L+   
Sbjct: 106 HEPGIDLAERLIKLAPVPMS-KVFFANSGSEANDTAVKLVWYYNNALGRPEKKKILSRVK 164

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
           A+HG T A  SLT      +D   P +  + H   P+ YR     +  E  ++   R+ +
Sbjct: 165 AYHGVTVATASLTGLVNNHRDFDLP-IARIQHTDCPHHYRFA---EPGESEEDFATRLAE 220

Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269
            +E  +     P  I A+F EP+ G GG +VPP  +F  ++    +Y ILL  DEV  G 
Sbjct: 221 SLEALILAE-GPETIAAMFAEPVMGAGGVIVPPATYFAKIQPILKKYDILLVADEVICGF 279

Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRADITFDK---PGRHATT 320
           GRTG FW  +  G++PD++   K +  G LP++ V     ++RA +   K      H  T
Sbjct: 280 GRTGNFWGSQTMGMQPDILTCAKQLSSGYLPISAVMVSDAVYRACVEESKKIGTFGHGYT 339

Query: 321 FGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378
           +  +PVA A  IE ++I +E  L+ HV+ V     + L+   + + ++G+ARG+GL  A+
Sbjct: 340 YSAHPVAAAVAIETLKIYEERDLVGHVRAVAPLFQRRLKALAD-HPLVGEARGVGLIGAL 398

Query: 379 EIVKSKETKEKY-PELRDRIVKE--SAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEI 435
           E+V  KETK  + P  R   V    S + GL++   GD S+   PPL++ +E+I+   + 
Sbjct: 399 ELVADKETKTPFDPVGRAGAVVNGLSQENGLIIRAMGD-SVAVCPPLVIGEEDINRMFDR 457

Query: 436 FEEALKAAL 444
              AL AA+
Sbjct: 458 LTTALDAAI 466


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: 544
Number of extensions: 32
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: 471
Length adjustment: 33
Effective length of query: 412
Effective length of database: 438
Effective search space:   180456
Effective search space used:   180456
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