Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 264 bits (674), Expect = 5e-75 Identities = 157/433 (36%), Positives = 235/433 (54%), Gaps = 22/433 (5%) Query: 16 KEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRV 75 KE+ +Y+A P + ++D DG DFA G+GV+N+GH HP+V Sbjct: 4 KELQALKERYVAAGAASPNEQ--FADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKV 61 Query: 76 VEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV 135 VEA+K Q +K H T YE + LAEKL + P KV+ NSGAEA E AMK+ Sbjct: 62 VEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIA 121 Query: 136 KYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPG-VTHIPYPNPYRNTWGI 194 + TG+ + F +HGRT +++ Q F P MPG V PYP PY Sbjct: 122 RAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGP-MPGTVYRAPYPVPYH----- 175 Query: 195 DGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFAD 254 G E + L ++ + P H AI EP+ GEGG+ P F K ++K D Sbjct: 176 -GVSEDEALRG-----LKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICD 229 Query: 255 EYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKP 314 E IL+ DEVQ G GRTGK +AIEH GVEPDL+ K++ G+P++ ++ D D Sbjct: 230 ENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIV-GTDKYMDAS 288 Query: 315 GRHAT--TFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDAR 370 G ++ T+ G+P A AA + V ++ KE +L Q +G+ L + +++E++ + + R Sbjct: 289 GPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVR 348 Query: 371 GLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEE 428 LG A E+V+SKE++ PEL + K++ ++GL+LL CG N++RF+ P+ + E Sbjct: 349 NLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLILLSCGMYGNTLRFLMPVTIEDEV 408 Query: 429 IDVAMEIFEEALK 441 ++ + I EE+LK Sbjct: 409 LEEGLAIVEESLK 421 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: 528 Number of extensions: 24 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: 445 Length of database: 425 Length adjustment: 32 Effective length of query: 413 Effective length of database: 393 Effective search space: 162309 Effective search space used: 162309 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