Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_001046645.1:WP_066609126.1 Length = 462 Score = 333 bits (853), Expect = 9e-96 Identities = 179/442 (40%), Positives = 265/442 (59%), Gaps = 13/442 (2%) Query: 16 LSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELV 75 + RDH + P T ++ GA ++ +G+++ D EG +++DA AGLWCVNVGYG++ + Sbjct: 12 IDRDHLIHPVTSFRGHEAHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIA 71 Query: 76 QAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVR 135 +AA QMR LP+ +F P V+LA+ + D++PEG++HV+FT GS+A D+ +R + Sbjct: 72 EAAAEQMRRLPYATGYFHFGSEPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYIT 131 Query: 136 HYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG 195 HY G+P+KK I GYHGS+ G L + H D P+ HIA PY Y Sbjct: 132 HYHNAIGKPEKKQFIALERGYHGSSSTGAGLTALANFHRGFDLPLRWQHHIASPYPY--R 189 Query: 196 GDMSPDEFGVWA--AEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILA 253 D+ D+ + A ++L+ K+ ++G +NVAAF EPIQG+GGVIVPP + +RE Sbjct: 190 SDLEGDDAAIIARSVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCT 249 Query: 254 KYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL 313 + DILF+ DEVI GFGRTG F + G PDLM +AKGLT+GY+PMG +++ ++ E + Sbjct: 250 QLDILFVTDEVITGFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGI 309 Query: 314 NQGG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADH 369 G HG TYSGHPV+AAV LE +R+ + I+ + A LA+H Sbjct: 310 ANGAAPEVAIGHGATYSGHPVSAAVGLEVLRLYTDGGILANGQ-RVATRFDAGLAGLANH 368 Query: 370 PLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCR--EHCFRNGLIMRAVGDTMI-IS 426 P+VG+ RG G++ A+ELV +K ++ RF D G+ + R + NG+I RA D +I ++ Sbjct: 369 PMVGDTRGRGLLGAIELVADKGSKARF-DPGLKLADRLFAKAYDNGVIFRAFADNIIGLA 427 Query: 427 PPLVIDPSQIDELITLARKCLD 448 P L ++DE+ K LD Sbjct: 428 PALCASDGEMDEIFARIAKTLD 449 Lambda K H 0.320 0.138 0.425 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: 566 Number of extensions: 23 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: 456 Length of database: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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