Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::pseudo5_N2C3_1:AO356_13150 (454 letters) >NCBI__GCF_001046645.1:WP_066609126.1 Length = 462 Score = 345 bits (885), Expect = 2e-99 Identities = 185/442 (41%), Positives = 268/442 (60%), Gaps = 13/442 (2%) Query: 14 LSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELA 73 + DH + P + F+ + G ++ KG++L D EG +++D AGLWCV VGYG++ +A Sbjct: 12 IDRDHLIHPVTSFRGHEAHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIA 71 Query: 74 DAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVR 133 +AA++QMR LPY +F P ++L++ + D++PEG++HV+FT GS+ D+ +R + Sbjct: 72 EAAAEQMRRLPYATGYFHFGSEPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYIT 131 Query: 134 HYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEG 193 HY G+P KK I+ + GYHGS+ GA L + H DLP+ HIA PY + Sbjct: 132 HYHNAIGKPEKKQFIALERGYHGSSSTGAGLTALANFHRGFDLPLRWQHHIASPYPY--R 189 Query: 194 GDMSPEEFGVWA--ANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILA 251 D+ ++ + A +L++K+ ++G DNV AF EPIQG+GGVIVPP + M+E Sbjct: 190 SDLEGDDAAIIARSVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCT 249 Query: 252 KYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVL 311 + DILFV DEVI GFGRTG F + G+ P +MT+AKGLT+GY+PMG L++ V + Sbjct: 250 QLDILFVTDEVITGFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGI 309 Query: 312 NEGG----DFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKRLRELNDH 367 G HG TYSGHPV+AAV LE +R+ D I+ A L L +H Sbjct: 310 ANGAAPEVAIGHGATYSGHPVSAAVGLEVLRLYTDGGILAN-GQRVATRFDAGLAGLANH 368 Query: 368 PLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQF--CFDNGLIMRAVGDTMI-IA 424 P+VG+ RG GLLGAIELV DK ++ R++ G+ + R F +DNG+I RA D +I +A Sbjct: 369 PMVGDTRGRGLLGAIELVADKGSKARFD-PGLKLADRLFAKAYDNGVIFRAFADNIIGLA 427 Query: 425 PPLVISKAEIDELVTKARHCLD 446 P L S E+DE+ + LD Sbjct: 428 PALCASDGEMDEIFARIAKTLD 449 Lambda K H 0.320 0.139 0.431 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: 593 Number of extensions: 23 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: 454 Length of database: 462 Length adjustment: 33 Effective length of query: 421 Effective length of database: 429 Effective search space: 180609 Effective search space used: 180609 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 (21.8 bits) S2: 51 (24.3 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