GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Halomonas xinjiangensis TRM 0175

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_043526888.1 JH15_RS03040 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_000759345.1:WP_043526888.1
          Length = 459

 Score =  188 bits (477), Expect = 4e-52
 Identities = 128/425 (30%), Positives = 225/425 (52%), Gaps = 32/425 (7%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF--- 95
           ++   +GI ++D +GN   D  +G+  +N+G+    +VEA   Q  +  +Y+  +FF   
Sbjct: 31  IVTHAQGIYIHDSEGNRILDGMAGLWCVNLGYGRAELVEAASAQMSQLPYYN--NFFKST 88

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFYH 149
           +  A+ LA+ L  LAPG + R V +  SG+EAN+  +++V      K    ++  +A  +
Sbjct: 89  HPPAVKLAKMLCGLAPGHMNR-VFFTGSGSEANDTVLRMVRRYWELKGQPDKRWVIARDN 147

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
           A+HG T A +SL     ++  G  P +P + HI  P      W  +G +   E   RV  
Sbjct: 148 AYHGSTVAGVSLGGMSPMRNQGG-PLVPDIAHIRQPY-----WFGEGRDMTPEAFGRVCA 201

Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269
              E     +    + A   EP+QG GG ++PP+ ++ A+K   D+Y ILL  DEV  G 
Sbjct: 202 ADLERKILELGVENVAAFIAEPVQGAGGAIIPPESYWPAIKAILDKYDILLVIDEVICGF 261

Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVI---HRADITFDKPGR--HATTFGG 323
           GR G+++  +H+ +EPDL+   K +  G LP+ GV+     AD   ++ G   H  T+ G
Sbjct: 262 GRLGEWFGSQHYSLEPDLMPVAKGLSSGYLPIGGVLVGDRVADTLIEEGGEFFHGFTYSG 321

Query: 324 NPVAIAAGIEVVEIVKE--LLPHVQ-EVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEI 380
           +PV     +  ++I+++  ++  V+ ++G YL K   E  E + ++G+AR LGL  A+E+
Sbjct: 322 HPVCATVALRNLQILRDEAVIDRVRDDIGPYLAKRWAELGE-HPLVGEARSLGLIGALEL 380

Query: 381 VKSKETKEKYPE---LRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFE 437
           V  K++ +++P+   + +     S  +GLV+   GD  I   PPL++  +++D  + +  
Sbjct: 381 VADKQSGQRFPQAFAVGNLCRDISFDKGLVMRSVGDTMI-ISPPLVIRHDQVDELVALAW 439

Query: 438 EALKA 442
           +AL A
Sbjct: 440 QALDA 444


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: 542
Number of extensions: 37
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: 459
Length adjustment: 33
Effective length of query: 412
Effective length of database: 426
Effective search space:   175512
Effective search space used:   175512
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 24 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