Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_058931225.1 AU252_RS13840 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_001484605.1:WP_058931225.1 Length = 410 Score = 261 bits (668), Expect = 2e-74 Identities = 138/394 (35%), Positives = 216/394 (54%), Gaps = 1/394 (0%) Query: 18 YEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAA 77 + + ++ +A ++ +RE+ +ISLAGG P + P+E +G+ ++ + Sbjct: 15 HTELWARRAAPTPSTAVREIFAAAARPGIISLAGGNPDVGSLPLEALGKTAAAIITGQGS 74 Query: 78 QALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIV 137 +ALQYG +G LR + M D+ T GSQ LD + ++ +PGD ++ Sbjct: 75 RALQYGAGQGTEELRSQICTVMSLEGINDADPDDVSVTIGSQSGLDTVTKILCDPGDTVL 134 Query: 138 VEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQN 197 + TY+ AL F YE + + D +G+ + L E++ L GK +K +YTIP F N Sbjct: 135 TDDATYMGALGTFSVYEVDVQPVLTDSDGLVPEALRERIDTLRGLGKHIKFLYTIPNFNN 194 Query: 198 PAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFS 257 P GVT++ +RR++++++ + + ++VEDNPYG LRY G+ + ++A + VIYL +FS Sbjct: 195 PTGVTLSLERRQQVVDICREANILVVEDNPYGLLRYRGDALPAMRAANPLD-VIYLSSFS 253 Query: 258 KILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEF 317 KI +PG R+GW PH ++ I +S LC F+Q++ Y+ + Sbjct: 254 KIFSPGLRLGWALVPPHLKQRFLIIGESSTLCPPAFNQMLTSAYLRDYDWQGQLEVSRAA 313 Query: 318 YKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEA 377 Y+ R DA L AL E MPDGV WT+PEGG F W TLP +DT+ ++ AV V Y PG A Sbjct: 314 YRLRSDAALSALSETMPDGVTWTRPEGGFFTWLTLPGAVDTQALITTAVDACVVYFPGAA 373 Query: 378 FFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411 F N +RL F+ + + I EGI RLA + Sbjct: 374 FSLGTAPSNQLRLAFSALSPDLITEGIHRLAPVL 407 Lambda K H 0.318 0.137 0.398 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: 425 Number of extensions: 22 Number of successful extensions: 4 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: 417 Length of database: 410 Length adjustment: 31 Effective length of query: 386 Effective length of database: 379 Effective search space: 146294 Effective search space used: 146294 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 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