Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_102106348.1 C0029_RS13280 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_002869505.1:WP_102106348.1 Length = 454 Score = 489 bits (1260), Expect = e-143 Identities = 240/453 (52%), Positives = 319/453 (70%), Gaps = 6/453 (1%) Query: 1 MNSQITNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMA 60 MN Q A T + L + HHL PFTD+K G R++++AE +YI+ +EG+K+LD M+ Sbjct: 1 MNMQ---ANTGNLKQLDQSHHLHPFTDFKDYATNGGRVMSRAEHIYIYTAEGHKMLDGMS 57 Query: 61 GLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFT 120 GLWC N+GY + +V A T Q+ +LP+YN FFQ ++ P +ELAKA+ D+ PE NHVFFT Sbjct: 58 GLWCCNLGYSQRSIVDAVTEQLGQLPYYNNFFQCSNQPAIELAKALVDITPERFNHVFFT 117 Query: 121 GSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPI 180 SGSEANDT LR+V Y+ +G+P+KK++I R N YHGST+A LGGM +HEQ + I Sbjct: 118 NSGSEANDTNLRLVSRYYQCQGRPEKKLIISRKNAYHGSTIAAACLGGMGPMHEQTN-GI 176 Query: 181 PGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVP 240 + HI QP+W+ G D P+EFG+ A QLE+KI E+GEENVAAFIAEP+QGAGGVI+P Sbjct: 177 DYVHHIEQPHWFEVGPDEDPNEFGLRVARQLEEKIDELGEENVAAFIAEPVQGAGGVIIP 236 Query: 241 PDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPM 300 PD+YWP+++ I + DIL IADEVICGFGRTG+W+GS+ YG PDLM AK +T+G+ P+ Sbjct: 237 PDSYWPEVQRICNERDILLIADEVICGFGRTGQWWGSETYGIEPDLMTFAKAVTNGFQPL 296 Query: 301 GGVVVRDEIVEV-LNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYL 359 GGV+V D++ +V L GEF HG TYSGHP AAA L + IL+E +I A AP+ Sbjct: 297 GGVMVADKVADVLLAHEGEFAHGLTYSGHPAAAAAGLATLNILKEGNVIADAAANIAPHF 356 Query: 360 QKRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGML-CREHCFRNGLIMRA 418 Q+R QELADH +VG+ RG GM AA+ELVK+K +RE + G L CR GL++R Sbjct: 357 QRRLQELADHKIVGQVRGRGMFAAVELVKDKSSREPLAAESAGALFCRNTANELGLMVRQ 416 Query: 419 VGDTMIISPPLVIDPSQIDELITLARKCLDQTA 451 G+ MI++PPL+ S+ID LI + + LD TA Sbjct: 417 TGNAMIMAPPLICSTSEIDSLIDMLGQALDVTA 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: 617 Number of extensions: 29 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: 454 Length adjustment: 33 Effective length of query: 423 Effective length of database: 421 Effective search space: 178083 Effective search space used: 178083 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