Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_013683113.1 ARCVE_RS02015 aminotransferase
Query= SwissProt::H3ZPU1 (389 letters) >NCBI__GCF_000194625.1:WP_013683113.1 Length = 384 Score = 332 bits (851), Expect = 1e-95 Identities = 179/384 (46%), Positives = 257/384 (66%), Gaps = 9/384 (2%) Query: 3 LSDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPN 62 +S R++ + PS IRK F+L G + +ISLG+GEPDF P I+E AL+KG+T Y+ N Sbjct: 8 VSKRVQELKPSGIRKFFELIIGRDDVISLGVGEPDFAVPWRIREEIIYALEKGITSYTSN 67 Query: 63 IGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFV 122 G+ ELREA+AE ++K G++ ++ ++IT G ++ + + L L + E VL+P P +V Sbjct: 68 FGLKELREAIAEYYRKF-GVECSAES-VLITTGVSEGVDIALRAILNEGEAVLVPEPCYV 125 Query: 123 SYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTP-KTRALIINTPNNPTGAVLTKKD 181 SYAP LAGG+ V +PT + F+LS + +++Y K +A++IN PNNPTG +KK+ Sbjct: 126 SYAPLSSLAGGEVVAIPTTPD--FKLSYELIDEYAKETKPKAIVINYPNNPTGVSYSKKE 183 Query: 182 LEEIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWR 241 LEEIAD A+EHD++++SDE+Y Y K+ SIASL+GM ER I +NGFSK FAMTG R Sbjct: 184 LEEIADAAIEHDMIVISDEIYAELSYT-FKHISIASLNGMEERAIILNGFSKAFAMTGLR 242 Query: 242 LGFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLV 301 +G+ AP ++E M++ Y C Q A +ALR+ +EEMR EY RRRN Sbjct: 243 IGYAIAPADILEGMLKIHQYCMLCAPVTAQIGALEALRNGED--ELEEMRAEYIRRRNFF 300 Query: 302 WKRLNEMGLPTVKPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYV 361 KR+ ++ L P GAFY FP I+ TGLSS+EF+E ++ E V VVPG+AFG+ GEGY+ Sbjct: 301 VKRVGKV-LDVKMPDGAFYAFPSIESTGLSSEEFAERLLFEKNVAVVPGNAFGECGEGYI 359 Query: 362 RISYATAYEKLEEAMDRMEKVLKE 385 R +YA + EKL EA+DR+ + ++E Sbjct: 360 RCAYAVSMEKLREAVDRIVEFVEE 383 Lambda K H 0.318 0.135 0.387 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: 410 Number of extensions: 13 Number of successful extensions: 6 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: 389 Length of database: 384 Length adjustment: 30 Effective length of query: 359 Effective length of database: 354 Effective search space: 127086 Effective search space used: 127086 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 10 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