Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= BRENDA::Q98TS5 (439 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 159 bits (401), Expect = 2e-43 Identities = 134/428 (31%), Positives = 196/428 (45%), Gaps = 62/428 (14%) Query: 59 PVALERGKGVYVWDVEGRRYFDFLSA-YSAVNQGHCHPKILDALKSQADKLTLTSRAFYN 117 P+ + G+G+ + D+ G+ Y D S VN G+ +I A+ Q + + +Y Sbjct: 35 PMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAVYEQ-----MKAMPYYA 89 Query: 118 DVLGE--YEEYITKIF----GYNKVLPMNTGVEGGETACKLARKWAYTVKGIPKYKAQII 171 G Y E+ K+ G + N+G E E A K+ R A+ + G P K +I+ Sbjct: 90 ATAGNIPYIEFAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAH-LSGNPA-KKKIL 147 Query: 172 FAAGNFWGRTMSAISSSTDPSSYEGFGPFMPGF--------------KIIPYNDLP---A 214 F A ++ G T+ A+SS+ E FGP +PGF K P D+ A Sbjct: 148 FRARDYHGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCARA 207 Query: 215 LERALQDPN---VAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLAR 271 +ER ++ V +VEPI GVI P Y T + +C H VL I DEV G+ R Sbjct: 208 VERIIEQEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGR 267 Query: 272 TGKMLAVDHENVRPDLVILGKALSGGVYPVSAVLCDDEVMLTI--KPGEHG------STY 323 TG M H V PD+V + K ++ P+S +EV P + STY Sbjct: 268 TGTMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTY 327 Query: 324 GGNPLGCRVAMASLEVIEEEKLAENANXMGELLRAELMKTPSDI--VTAVRGKGLLNAIV 381 GG GC A+ ++ +IEEEKL +N N MG+ L A L K D+ V VRGKGLL I Sbjct: 328 GGCAAGCSAALENMAIIEEEKLLDNVNAMGDYLLAGL-KELGDLPYVGDVRGKGLLCGIE 386 Query: 382 IKQSK-------DCDAWKVCLRLRDNGLL------AKPTHGDIIRLAPPLTIKEDEIREC 428 + Q K + +V + N +L + P +II +AP + D I Sbjct: 387 LVQDKAGKKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNI--- 443 Query: 429 SEIIHKTL 436 ++I +TL Sbjct: 444 -DVILRTL 450 Lambda K H 0.318 0.136 0.404 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: 490 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: 439 Length of database: 459 Length adjustment: 33 Effective length of query: 406 Effective length of database: 426 Effective search space: 172956 Effective search space used: 172956 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.
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