Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate H281DRAFT_01831 H281DRAFT_01831 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain
Query= reanno::acidovorax_3H11:Ac3H11_1015 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_01831 Length = 414 Score = 342 bits (877), Expect = 1e-98 Identities = 178/397 (44%), Positives = 257/397 (64%), Gaps = 10/397 (2%) Query: 2 QFADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAAL 61 +F N S IRELFK LG+PG+ISFAGG+P S +FDV+G++ A A ++P + L Sbjct: 14 EFTAPFQNPSGSPIRELFKYLGEPGMISFAGGYPASDLFDVDGLQQAEARAY-QDPNSCL 72 Query: 62 QYGATEGYNPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEG 121 QYG T+G L+ +L + M +G A + ++VTTGSQQ LDLL + L+SPGD V E Sbjct: 73 QYGPTDGLPRLKHELISLMARRGVP-CALNEMLVTTGSQQGLDLLLRVLVSPGDVVFTEQ 131 Query: 122 PTFLATIQCFRLYGAELISAPIDGNGVKTDELEKLIAEHK---PKFVYLIPTFGNPSGAM 178 P + AT+Q +L A++++ P+D +G+ D L +L+A + PK +Y +PTF NP+GA Sbjct: 132 PAYPATLQALKLQQAKIVTVPVDAHGLDVDHLAELLASGRVARPKLLYTVPTFANPTGAT 191 Query: 179 LSLERRKAVLEMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLS 238 ++ ERR A+L++AV++ LIVEDDPYGDL F PS+++L+A V GSR+ +VH SLS Sbjct: 192 ITRERRIALLKLAVQYKFLIVEDDPYGDLRFSGVAVPSIISLAAEVEGSRDWVVHFASLS 251 Query: 239 KVLSPGLRVGWMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKV 298 K+++PGLRVGW IAPAE+ + + KQ D ++ + QA AA+YL G + L + ++ Sbjct: 252 KIVAPGLRVGWTIAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITEM 311 Query: 299 YAERAQAMGDALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFV 358 Y + +A+ +ALR + GD ++F +P GG+FVWAR+ G D + L + AIE V FV Sbjct: 312 YGRKCEALCEALRSQFGDTLQFHRPDGGMFVWARIEG-----IDASALLQHAIENKVMFV 366 Query: 359 PGTPFFCANPDHATFRLSFATADVDKIREGVARLGQA 395 PG FF D A+ RLSFA + I EG RL +A Sbjct: 367 PGKAFFADRIDPASLRLSFAAPGIADIEEGAKRLRRA 403 Lambda K H 0.319 0.136 0.394 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: 504 Number of extensions: 30 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: 396 Length of database: 414 Length adjustment: 31 Effective length of query: 365 Effective length of database: 383 Effective search space: 139795 Effective search space used: 139795 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 17 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