Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_078427037.1 BK574_RS00545 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_002019605.1:WP_078427037.1 Length = 449 Score = 177 bits (449), Expect = 6e-49 Identities = 126/425 (29%), Positives = 218/425 (51%), Gaps = 33/425 (7%) Query: 35 NLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDF 94 N PI I+ G+G+ +YD+DG + D +SG N+GH +V A+ +Q++K + + F Sbjct: 14 NYPI-IDSGKGVFLYDIDGKDYLDASSGAVTANIGHGVEEIVNAMHEQSKKVSFVYRSQF 72 Query: 95 FYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKL-VKYGTGRKQ-----FLAFY 148 + A LAEKL +++PG + + NSG EA E AMK+ +++ RK+ FL+ Sbjct: 73 TNQPAEELAEKLSDISPGTLNWSF-FVNSGTEAIETAMKVALQHWQERKRPEKQLFLSRR 131 Query: 149 HAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVL 208 ++HG T LSL+ +++ F P + + P YR + + + + Sbjct: 132 LSYHGITVGALSLSGFI-TRRERFEPLLENYPLLSPPYCYRCPFHSSYPKCHLQCAEELE 190 Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGE-GGYVVPPKGFFKALKKFADEYGILLADDEVQM 267 D IE ++ I A EPI G GG + PP G+++ +++ + + IL DEV Sbjct: 191 DVIERLGAKY-----IAAFVAEPIIGAAGGAITPPDGYYQKIQEICNRHEILFIADEVMT 245 Query: 268 GIGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI--TFDKPGR---HATTF 321 G+GRTGK +A+EH+GV PD++ GK + GG P+A + ++ +K + TF Sbjct: 246 GMGRTGKMFAVEHWGVTPDIMAIGKGLSGGYTPIAATLVSDEVIEPIEKGSKVIMSGHTF 305 Query: 322 GGNPVAIAAGIEVVE--IVKELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVE 379 NP + A + V++ + ++ +V E G+ L L +++ IGD RG GL +E Sbjct: 306 SANPQSCATALAVIQYTLKNNIIDNVTERGEMLKTKLAPLMKRFSFIGDVRGKGLLLGME 365 Query: 380 IVKSKETKEKYP---ELRDRIVKESAKRGLVLL-------GCGDNSIRFIPPLIVTKEEI 429 V++ K+ +P + ++ + + L+L G +N + PPL +T +EI Sbjct: 366 FVENARLKKTFPRDWNISQMVIDHAMESQLLLYPAASGHNGLDNNGVLLAPPLTITNKEI 425 Query: 430 DVAME 434 D+ +E Sbjct: 426 DLLVE 430 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: 488 Number of extensions: 24 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: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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