Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__WCS417:GFF1577 Length = 389 Score = 129 bits (323), Expect = 2e-34 Identities = 125/412 (30%), Positives = 189/412 (45%), Gaps = 37/412 (8%) Query: 35 IVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPS 94 + L TR G+ L D GR YLD VA + +G + P LV A + + A Sbjct: 13 LALSFTRGLGTRLWDQ-QGREYLDAVAGVAVTNVGHSHPRLV------AAISEQAGLLLH 65 Query: 95 NSDVYSVA-MARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGID 153 S++YS+ R + ++ G L FF GA A E ALK A H GI+ Sbjct: 66 TSNLYSIDWQQRLAQRLTQLSG---LDRAFFNNSGAEANETALKLA----RLHGWKKGIE 118 Query: 154 PALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAAL 213 L V+ + AFHGR+ TL+ ++ P++ F + + +++ + +AAL Sbjct: 119 APL---VVVMENAFHGRTLGTLAASDG-PSVRLGFQQ-----LPGDFLKVRFGD--LAAL 167 Query: 214 EAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEV 273 EA AF R I + EPIQGE G + A+R+ C L++ DE+ Sbjct: 168 EA-----ITKAFGPR---ITAVLLEPIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEI 219 Query: 274 QTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGG 333 QTG G TGT +A+Q + PD++ K GV G + A P ST+GG Sbjct: 220 QTGIGRTGTWFAFQHEGIVPDVMTLAKGLG-NGVPIGACLARAAVAQLFTPGSHGSTFGG 278 Query: 334 NLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSL 393 N +L++IE +GL + A Q G+ L ARL + + A V+ RG+GLM L Sbjct: 279 NPLACRVGCTVLDIIEEQGLLQNAAQQGERLLARL-RVELNEHAQVVAIRGQGLMIGIEL 337 Query: 394 PTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSAL 445 + RD R + +++ +R PPLT+ T E++ + A+ L Sbjct: 338 ASPC-RDLAQRAAQEHGLLINVTRGKIIRLLPPLTLDTQEVEMIVRAITRLL 388 Lambda K H 0.323 0.137 0.412 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: 351 Number of extensions: 20 Number of successful extensions: 3 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: 449 Length of database: 389 Length adjustment: 32 Effective length of query: 417 Effective length of database: 357 Effective search space: 148869 Effective search space used: 148869 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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