Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_000009985.1:WP_011384093.1 Length = 459 Score = 372 bits (954), Expect = e-107 Identities = 200/450 (44%), Positives = 275/450 (61%), Gaps = 7/450 (1%) Query: 6 TNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCV 65 T+A R D L P+T+ K+ E G +IT+ +GV ++D G ++ +AGLWC Sbjct: 3 THASNRTIAEKDVDSVLHPYTNLKRHPEVGPLVITRGQGVRVYDEAGRDYIEGLAGLWCT 62 Query: 66 NVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSE 125 ++G+G E LV+AA RQMR+LPFY+LF H VEL + +AP M+ VF GSGSE Sbjct: 63 SLGWGEERLVEAAARQMRQLPFYHLFSHKTHDVGVELCARLLAMAPVPMSKVFLAGSGSE 122 Query: 126 ANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVH 185 ANDT ++++ + G P KK +I R YHG TVA SL G+ D PIPG++ Sbjct: 123 ANDTAIKLIHYRANALGTPDKKKIIAREKAYHGVTVATASLTGLVNNQRSFDLPIPGVLR 182 Query: 186 IAQPYWYGEGGD-MSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTY 244 A P+ Y D S ++F A +LE IL G + VAAF AEP+ GAGGVIVPP Y Sbjct: 183 AACPHHYRFAKDGESEEDFSTRLAGELEAMILAEGPDTVAAFFAEPVMGAGGVIVPPAGY 242 Query: 245 WPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVV 304 +PKI+ +L +YD+L + DEVICGFGRTG+ FG++ +G PD+M +AKGL+SGY P+ ++ Sbjct: 243 FPKIQAVLDRYDVLLVVDEVICGFGRTGKMFGTETFGIRPDMMTLAKGLSSGYAPISALM 302 Query: 305 VRDE----IVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQ 360 V + + E + G F HG+TY GHPV+AAVALE + I E I+ +V AE P LQ Sbjct: 303 VNERVYGPVAEESGRIGVFGHGYTYGGHPVSAAVALETLNIYAERDILAQV-AEVGPVLQ 361 Query: 361 KRWQELADHPLVGEARGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAV 419 + L HPLVGEARGVG++ A+ELV +K R F + VG G+I+RA+ Sbjct: 362 DGLRALRGHPLVGEARGVGLIGAVELVADKANRAPFPPELAVGARVVAKAQAKGVILRAM 421 Query: 420 GDTMIISPPLVIDPSQIDELITLARKCLDQ 449 GD + +PPLVI + I E++ LD+ Sbjct: 422 GDAVAFAPPLVISKADIAEMLRRFGLALDE 451 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: 612 Number of extensions: 24 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: 459 Length adjustment: 33 Effective length of query: 423 Effective length of database: 426 Effective search space: 180198 Effective search space used: 180198 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 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