Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate 202600 SO3497 aminotransferase, class III (NCBI ptt file)
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__MR1:202600 Length = 446 Score = 177 bits (450), Expect = 5e-49 Identities = 130/424 (30%), Positives = 216/424 (50%), Gaps = 29/424 (6%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 ++ +AEG+Y+ D++GN +LD ++G+ N G ++ EA+ KQ+ + +A +P Sbjct: 34 LLAQAEGMYYTDINGNKVLDSTAGLWCCNAGHGRREISEAVSKQIRQMDYAPSFQMGHPI 93 Query: 99 QVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA------KWSTNRKMFIAFIGAFH 152 ELA++L E++P + KVF +NSG+E+ + ALK+A +R FI +H Sbjct: 94 AFELAERLTELSPEGLN-KVFFTNSGSESVDTALKMALCYHRANGQASRTRFIGREMGYH 152 Query: 153 GRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIE 212 G G +S+ +++ + GV H+P+ ++ G + L + +E Sbjct: 153 GVGFGGISVGGLSNNRKAFSGQLLQGVDHLPHTLDIQHAAFSRGLPS---LGAEKAEVLE 209 Query: 213 EYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGR 272 + + H AE +A + EP+ G G ++PP+ + K L+++ KHGILLI DEV GR Sbjct: 210 QLVTLH--GAENIAAVIVEPMSGSAGVILPPQGYLKRLREITKKHGILLIFDEVITAFGR 267 Query: 273 TGRMWAIEHFDIVPDIVTVAKAL-GGGIPIGATIFRADL--DFGVSG-------VHSNTF 322 G +A + + ++PDI+T AKA+ G IP+GA +F D D + G H T+ Sbjct: 268 VGAAFASQRWGVIPDIITTAKAINNGAIPMGA-VFVQDYIHDTCMQGPTELIEFFHGYTY 326 Query: 323 GGNTVAAAAALAVIEELQN-GLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVE 381 G+ VAAAAALA + QN L E + +LE F E + +K +I D+R GL G + Sbjct: 327 SGHPVAAAAALATLSIYQNEQLFERSFELERYFEEAVHSLKGLPNVI-DIRNTGLVAGFQ 385 Query: 382 FVKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDIFEEA 441 + + +RG V E L+ I + PPLI+ + + ++ +A Sbjct: 386 LAPNSQ----GVGKRGYSVFEHCFHQGTLVRATGDIIAMSPPLIVEKHQIDQMVNSLSDA 441 Query: 442 IKVV 445 I V Sbjct: 442 IHAV 445 Lambda K H 0.319 0.139 0.410 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: 508 Number of extensions: 23 Number of successful extensions: 4 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: 454 Length of database: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 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 09 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