GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Shewanella amazonensis SB2B

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 6938540 Sama_2643 putative aminotransferase (RefSeq)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__SB2B:6938540
          Length = 460

 Score =  193 bits (490), Expect = 1e-53
 Identities = 136/429 (31%), Positives = 224/429 (52%), Gaps = 34/429 (7%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF--- 95
           VIER EG+ ++D  GN   D  +G+  +NVG+    + +A   Q +    Y+  +FF   
Sbjct: 37  VIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPFYN--NFFQCT 94

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFYH 149
           +E AI LA K+  LAPG + R V +  SG+EAN+  +++V      K    +K  ++  +
Sbjct: 95  HEPAIRLASKIASLAPGHMNR-VFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKN 153

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYE-EPDELTNRVL 208
           A+HG T A  SL    ++ Q G  P +PG+ HI  P      W  +G +  P+    +  
Sbjct: 154 AYHGSTVAGASLGGMGFMHQQGDLP-IPGIVHIDQPY-----WFGEGRDMSPEAFGIKTA 207

Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268
             +E  +   +   ++ A   EP QG GG ++PP  ++  +K+  ++Y IL   DEV  G
Sbjct: 208 QALEAKILE-LGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFILDEVISG 266

Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVI---HRADITFDKPGR--HATTFG 322
            GRTG ++A +  G++PDLI   K +  G +P+ GVI     AD+     G   H  T+ 
Sbjct: 267 FGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYS 326

Query: 323 GNPVAIAAGIEVVEIVKE--LLPHVQ-EVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVE 379
           G+PVA A  +E + I++E  L+  V+ + G YL   L+     + ++G+ RG+G+  A+E
Sbjct: 327 GHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTL-SAHPLVGEVRGMGMVGAIE 385

Query: 380 IVKSKETKEKY-PELRDRIVKESA--KRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIF 436
           +V  K +  ++  E+   ++   A  + GLV+   GD  I   PPL +T++EID  +   
Sbjct: 386 LVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI-ISPPLCITRDEIDELIFKA 444

Query: 437 EEALKAALK 445
            +AL   L+
Sbjct: 445 SQALSLTLE 453


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: 475
Number of extensions: 30
Number of successful extensions: 6
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: 460
Length adjustment: 33
Effective length of query: 412
Effective length of database: 427
Effective search space:   175924
Effective search space used:   175924
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