Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_048038594.1 MM_RS12280 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::H3ZPU1 (389 letters) >NCBI__GCF_000007065.1:WP_048038594.1 Length = 370 Score = 288 bits (738), Expect = 1e-82 Identities = 157/380 (41%), Positives = 246/380 (64%), Gaps = 16/380 (4%) Query: 4 SDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPNI 63 S+ + ++ S IRK+F+ A I+LG+G+PDFDTP+HIK A +A+++G T Y+ Sbjct: 7 SENVSRIDTSGIRKIFEAAGS--NAINLGLGQPDFDTPDHIKAAAIKAINEGFTGYTAGP 64 Query: 64 GILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFVS 123 GI ELREA+++KFK+ N P+ +I++T G ++ + + L L +EVLI +P FVS Sbjct: 65 GIPELREALSQKFKEENCFSVSPQ-EIIVTSGASEALTIALTALLNRGDEVLISNPGFVS 123 Query: 124 YAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDLE 183 Y + GK V VP E+ + +++ + +TPKT+A+I+N+P+NPTGAV ++ D++ Sbjct: 124 YNALTEMLYGKVVNVPLGED--LTMKPEDVLERITPKTKAIILNSPSNPTGAVSSRADIK 181 Query: 184 EIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRLG 243 +A+ A +H + I+SDEVYEYF+Y+G ++ S AS + +T+N SK++AMTGWRLG Sbjct: 182 ALAEIADDHRITIISDEVYEYFIYEG-EHVSPASYS---DNVVTVNATSKSYAMTGWRLG 237 Query: 244 FLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLVWK 303 +LAA + +M++ Y C + Q AA A+ + +V MR E+ +RR+++ K Sbjct: 238 YLAARNEYISQMLKVHQYIQACANSIAQKAAYAAVTGPK--DSVSAMREEFRKRRDVLVK 295 Query: 304 RLNEMGLPTVKPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYVRI 363 LN++G+ PKGAFY FPR+ +S E + MI VVVVPG+AFG G+GY+RI Sbjct: 296 GLNDLGMECALPKGAFYAFPRVS----NSAEVASKMISNG-VVVVPGTAFGSEGDGYIRI 350 Query: 364 SYATAYEKLEEAMDRMEKVL 383 SYA + + +E+++ MEKVL Sbjct: 351 SYAASMKDIEKSLSIMEKVL 370 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: 352 Number of extensions: 16 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: 370 Length adjustment: 30 Effective length of query: 359 Effective length of database: 340 Effective search space: 122060 Effective search space used: 122060 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 Jul 25 2024. The underlying query database was built on Jul 25 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