Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_051305361.1 G494_RS0103960 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_000429965.1:WP_051305361.1 Length = 466 Score = 220 bits (560), Expect = 9e-62 Identities = 137/449 (30%), Positives = 234/449 (52%), Gaps = 27/449 (6%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78 HHL P +K + II + +G+ + D GN+ LDA +G +W V VGYGR+ + +A Sbjct: 25 HHLKP---HKVFDNAEQMIIVEGQGLMVKDIRGNEYLDATSGGVWSVMVGYGRDSIAEAV 81 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 Q++++P++ F + P ++ A+ + + P M+ V+F+ SGSEAN+ ++VR Sbjct: 82 CAQLKKMPYFAGVF--GNVPSIKFAQKLLEKLPR-MDKVYFSNSGSEANEKAFKIVRQ-- 136 Query: 139 ATKGQPQKK---VVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG 195 A++ P++K ++ R YHG+T+ +S G + + G V Y Sbjct: 137 ASRISPERKGKYKIMYRDRDYHGTTIGAMSATGQAQRKQDFGPFVEGFVEFPHCACYRCP 196 Query: 196 GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255 D + E + A ++E IL+ G + + A I EPI GG++ P Y+P ++EI KY Sbjct: 197 HDKTYGECNIECARKVEDIILKEGADTIGAMIVEPITAGGGILKPVPEYYPILQEICKKY 256 Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEV-LN 314 DI I DEV+CGFGRTG+++G +++ PD++ +AKGL S Y + VV+ + +V LN Sbjct: 257 DIWMIMDEVVCGFGRTGKFWGHEHFDVDPDIVTMAKGLASSYEALSATVVKQHVYDVFLN 316 Query: 315 QGGE-------FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELA 367 F TY G A ALE+ RI+ +E ++E + E Y+ + +EL Sbjct: 317 DPANEDDRLNYFRDISTYGGCTSAMTAALESTRIIEDENLVENSR-EIGAYMISKLEELK 375 Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMR------AVGD 421 VG+ RG G+ +E V N++T+E T+ + L + ++ R + + Sbjct: 376 KFDCVGDIRGEGLFGGIEFVTNRETKEPITEGQMAALMGNVMAQGVIVGRTNSSFHGLNN 435 Query: 422 TMIISPPLVIDPSQIDELITLARKCLDQT 450 M +P L+I Q+D ++ +++T Sbjct: 436 IMNFAPCLIITKEQVDTVVGAVAAAIEKT 464 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: 528 Number of extensions: 34 Number of successful extensions: 5 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: 466 Length adjustment: 33 Effective length of query: 423 Effective length of database: 433 Effective search space: 183159 Effective search space used: 183159 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