Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_078717318.1 B5D49_RS08760 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_900167125.1:WP_078717318.1 Length = 394 Score = 299 bits (766), Expect = 9e-86 Identities = 159/396 (40%), Positives = 246/396 (62%), Gaps = 7/396 (1%) Query: 19 EKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQ 78 ++ F+++ + S IRE+LK+ +IS AGGLP PE FP + I E + L Sbjct: 2 QETFAKRMGKVHRSFIREILKVTADPSIISFAGGLPNPECFPSKAIAEAAQRALTNAPVS 61 Query: 79 ALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVV 138 ALQY T+G LR +AE +R + + DI+ T+GSQQ +D++ +VF++ GD +V+ Sbjct: 62 ALQYAPTEGDPELRAWIAERYDQRMGLKLDPDDILITTGSQQCVDMVAKVFLDQGDTVVL 121 Query: 139 EAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNP 198 E P YL A+Q+F +EP+F IPL ++G ++D LE L E K+ Y +P FQNP Sbjct: 122 ERPAYLGAIQSFSVFEPQFRTIPLLEDGPDLDALEALLDE-----APAKLFYAVPNFQNP 176 Query: 199 AGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSK 258 +G++ + ++R+ + EL + + VED+PYGELR+ GE + + + EG+ I +G+FSK Sbjct: 177 SGLSYSLEKRRAVAELCLRRGLLFVEDDPYGELRFKGEHLPSVYTF-AEGQSILMGSFSK 235 Query: 259 ILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFY 318 I PGFR+GWI A L KQ+ DL T + +Q I + ++ +D HI I E Y Sbjct: 236 IATPGFRLGWIVARGDVRDALIRVKQASDLHTPSLTQRIMVELLQHFDMDAHIAMIRERY 295 Query: 319 KPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAF 378 +R+ M++A+ E P+GV ++PEGGMF+W TLP+G + +++KAVA VA+VPG+ F Sbjct: 296 GHQRNVMVEAIREHFPEGVTISEPEGGMFLWVTLPQGCSSMQLMDKAVACKVAFVPGKPF 355 Query: 379 FAH-RDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 + + +NT+RLNF+ EE IREG+ RL + ++E Sbjct: 356 YVDPGEGENTLRLNFSNASEEMIREGVARLGKALQE 391 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: 455 Number of extensions: 25 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: 394 Length adjustment: 31 Effective length of query: 386 Effective length of database: 363 Effective search space: 140118 Effective search space used: 140118 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