Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_011033973.1 MM_RS10585 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::H3ZPU1 (389 letters) >NCBI__GCF_000007065.1:WP_011033973.1 Length = 393 Score = 342 bits (878), Expect = 8e-99 Identities = 162/377 (42%), Positives = 254/377 (67%), Gaps = 3/377 (0%) Query: 3 LSDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPN 62 +++ ++ + PS IR+ FDL G+E IISLG+GEPDF TP HI+E +L+KG T Y+ N Sbjct: 11 IAEAVKSIPPSGIRRFFDLVSGLEDIISLGVGEPDFITPWHIREMCIHSLEKGQTSYTSN 70 Query: 63 IGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFV 122 G+ ELR+ + + + G+D +P+++I+IT G ++ + + + + +EV++ P +V Sbjct: 71 SGLPELRDELTRTYYRRYGLDYNPESEILITTGVSEALDIAIRAVVNPGDEVIVVQPSYV 130 Query: 123 SYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDL 182 +Y P+VI+AGGKPV V T+ +++F L+ + LE +T KT+A+++N PNNPTGA++ K+ + Sbjct: 131 AYVPSVIMAGGKPVIVSTHRDDDFSLTAEVLEPAITSKTKAIVLNFPNNPTGAIMQKEGM 190 Query: 183 EEIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRL 242 E+IAD VE+DL ++SDEVYE Y+G + +SL+GM +RT+ +NGFSK +AMTG RL Sbjct: 191 EDIADLVVENDLFLISDEVYECLTYEGT-HVPFSSLEGMKDRTVMLNGFSKAYAMTGLRL 249 Query: 243 GFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLVW 302 GF ++ M+ Y C Q A +ALR+ + +E M REY+RRR+ + Sbjct: 250 GFAMGAPDIIHSMMMIHQYCMLCAPITAQVGAIEALRNGKG--EMERMVREYDRRRHFIV 307 Query: 303 KRLNEMGLPTVKPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYVR 362 N +GL PKGAFY FP I DTGLSS +F+E ++ E K+V +PG FG+AGEG++R Sbjct: 308 NGFNRIGLECCNPKGAFYAFPYIGDTGLSSSDFAERLLNEKKIVTIPGDVFGEAGEGFLR 367 Query: 363 ISYATAYEKLEEAMDRM 379 +YA + + +++A++RM Sbjct: 368 CAYAASLDDIKKAIERM 384 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: 363 Number of extensions: 15 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 358 Effective length of database: 362 Effective search space: 129596 Effective search space used: 129596 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