Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_012674835.1 SULAZ_RS03325 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000021545.1:WP_012674835.1 Length = 386 Score = 234 bits (596), Expect = 5e-66 Identities = 155/432 (35%), Positives = 237/432 (54%), Gaps = 58/432 (13%) Query: 18 VIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVE 77 +IE+ KYL Q+ LP E+GEG +YD G + D SG+ V +G++HP++ + Sbjct: 1 MIEKASKYLF---QNYGRLPYFFEKGEGCYLYDDKGKKYLDMLSGIAVNALGYNHPKLTK 57 Query: 78 AIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK- 136 AI +QA K H S + FY I K+ L+ KV + NSGAE+NEA +KLV+ Sbjct: 58 AICEQASKIIHIS--NLFYIKPQIEVAKI--LSENSFGGKVFFCNSGAESNEALIKLVRR 113 Query: 137 YGTGRKQ----FLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTW 192 Y +KQ + F +FHGRT A ++ TA +GF+P + G + + Sbjct: 114 YFYDKKQERYEIITFEGSFHGRTLATVTATAQP-KYHEGFYPLVEGFKYAKF-------- 164 Query: 193 GIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKF 252 + D + N + D + AI E +QGEGG K F K L K Sbjct: 165 -----NDIDSVKNLITD-------------KTAAILIELVQGEGGVNPANKEFIKELYKL 206 Query: 253 ADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD 312 E IL DEVQ GIGRTGK +A +HF ++PD+I K +GGG+P+ +I + DI Sbjct: 207 CKENDILFTVDEVQTGIGRTGKLFAYQHFDIQPDIISLAKGLGGGVPIGAIIAKDDIAKS 266 Query: 313 -KPGRHATTFGGNPVA-IAAGIEVVEIVKE-LLPHVQEVGDYLHKYLEEFKEKYEVIG-D 368 PG HA+TFGGN ++ +AA + + E++ E L VQ+VG+YL KE ++ G Sbjct: 267 FVPGTHASTFGGNYLSTVAAKVVLEEVLSEGFLDRVQKVGEYL-------KEALKIFGYP 319 Query: 369 ARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEE 428 +GLGL +++ +S KE ++K++ ++GL++ G+N++RF+PPLI+T++E Sbjct: 320 VKGLGLMVGMDLPQSISAKE--------VMKKTLEKGLIVGTAGENTLRFVPPLIITEKE 371 Query: 429 IDVAMEIFEEAL 440 +D A++I +E L Sbjct: 372 VDEAVDILKEVL 383 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: 482 Number of extensions: 24 Number of successful extensions: 7 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: 386 Length adjustment: 31 Effective length of query: 414 Effective length of database: 355 Effective search space: 146970 Effective search space used: 146970 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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