Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_900156495.1:WP_076477443.1 Length = 389 Score = 265 bits (676), Expect = 2e-75 Identities = 148/388 (38%), Positives = 231/388 (59%), Gaps = 20/388 (5%) Query: 29 MKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGF 88 ++ S IR+LL++ E DV+S+AGGLPA + P + I E V+ + A ALQY + G Sbjct: 15 IRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISE--ASALQYTVSAGV 72 Query: 89 TPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148 PLR +A+ + ++ T GSQQAL L + ++PGD ++V+ P Y+ ALQ Sbjct: 73 RPLREVVADRDGTHPE------RVLITHGSQQALFLSAQALLDPGDTVIVDDPVYVGALQ 126 Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208 F+ E V +P+ EG +VD LE L + G + +IV+T+ F NPAGVT + + R Sbjct: 127 VFQSVRAEIVALPITAEGTDVDRLERLLSD----GVRPRIVHTVSNFHNPAGVTASARTR 182 Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268 +RL ELA+ + F I+ED+PYG+LR++G + PI RVI LG+ SKILAP R+GW Sbjct: 183 RRLAELAADHGFWIIEDDPYGQLRFAGRSMDPIPG----DRVIRLGSASKILAPALRVGW 238 Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYV-EGGYLDKHIPKIIEFYKPRRDAMLK 327 + A P + +E+ +Q DLC +TF+Q++ + + ++ H+ + Y R A+ Sbjct: 239 LQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARRAAALTG 298 Query: 328 ALEEFMPD--GVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVK 385 AL + GV++ +PEGGMF W LP G+DT ++L+ AV GVA+VPG AF + Sbjct: 299 ALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFAVDAGLG 357 Query: 386 NTMRLNFTYVPEEKIREGIKRLAETIKE 413 + +RL+F + +++ E ++RLA + + Sbjct: 358 DRLRLSFATLSPDQLTEAVRRLATAVHD 385 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: 326 Number of extensions: 14 Number of successful extensions: 7 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: 389 Length adjustment: 31 Effective length of query: 386 Effective length of database: 358 Effective search space: 138188 Effective search space used: 138188 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