Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_012386117.1 BIND_RS16265 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::H3ZPU1 (389 letters) >NCBI__GCF_000019845.1:WP_012386117.1 Length = 410 Score = 190 bits (482), Expect = 7e-53 Identities = 120/387 (31%), Positives = 205/387 (52%), Gaps = 20/387 (5%) Query: 13 SEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPNIGILELREAV 72 S I ++F +G +G+I L +GE D TP I E A +L +G T Y+ G+ ELR A+ Sbjct: 28 SGIVEVFAYGRGRQGLIPLFVGEGDLPTPPFIVEAASRSLTEGETFYTYQAGVPELRAAI 87 Query: 73 AEKFKKHNG------IDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFVSYAP 126 A +H G + Q +T+G + + L + +EEV++P+P + ++ Sbjct: 88 AAYMSRHYGAIYERTVAPFSPEQFFVTIGGMHALQIALRLVARADEEVIVPTPAWPNFHG 147 Query: 127 AVILAGGKPVEVPTYEENE----FRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDL 182 A+ + G +P+ VP +N + L D +E +TP TR LI+NTP+NPTG V + KDL Sbjct: 148 ALSVLGARPITVPMLFQNNGSPGWTLDFDRIEASITPATRCLIVNTPSNPTGWVASLKDL 207 Query: 183 EEIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRL 242 E + H L +++DE+Y ++G + S + + + + FSK +AMTG RL Sbjct: 208 ETLLALTRRHGLWLVADEIYGRMTFNGERAPSFHDIMEKDDNILFLQTFSKNWAMTGLRL 267 Query: 243 GFLAAPEW---VVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRN 299 G+L AP ++E ++++ P Q AA AL E+ ++ R + R Sbjct: 268 GWLEAPRSLAPIIENLIQYSTSGVAVP---WQRAATVAL--EQGEDFFQQSLRRIHQGRT 322 Query: 300 LVWKRLNEMG-LPTVKPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGE 358 ++++ L + G + +P+GAFY+F ++ +++ + +I EA V V PG+AFG GE Sbjct: 323 ILYEGLKKTGRIIAAEPEGAFYLFCKVMGE-TDTRQLALRLIDEANVGVAPGTAFGPGGE 381 Query: 359 GYVRISYATAYEKLEEAMDRMEKVLKE 385 ++R+ +A L EA+ R+ L++ Sbjct: 382 EFLRLCFARDPALLTEAVRRLSLWLEQ 408 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: 339 Number of extensions: 16 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: 389 Length of database: 410 Length adjustment: 31 Effective length of query: 358 Effective length of database: 379 Effective search space: 135682 Effective search space used: 135682 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