Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_047216723.1 PATSB16_RS17975 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_001931675.1:WP_047216723.1 Length = 433 Score = 275 bits (703), Expect = 2e-78 Identities = 156/440 (35%), Positives = 236/440 (53%), Gaps = 25/440 (5%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT ++ ++ R++ KAEG+Y +G ++LD AGLWCVN G+ R E+V+A Q+ Sbjct: 7 PFTANREF-KRAPRLLVKAEGMYYTSHDGRQVLDGTAGLWCVNAGHCRREIVEAVRAQVG 65 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 E+ F F Q HP E A +A++ P + +FFT SGSE+ DT L++ Y +G+ Sbjct: 66 EMDFAPTF-QMGHPKAFEAAAKLAELTPGDLKRIFFTNSGSESVDTALKIALAYHRARGE 124 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQ-GDFPIPGIVHIAQPYWYGEGG-DMSPD 201 Q+ IGR GYHG G+S+GG+ + +P + H+ E Sbjct: 125 GQRTRFIGRERGYHGVGFGGISVGGIAPNRKTYSGALLPAVDHLPHTLNLAEAAFTRGQP 184 Query: 202 EFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIA 261 +G A++LE+ ++ +AA I EP+ G+ GV+VPP Y ++R+I K+ IL I Sbjct: 185 AWGAHLADELERLVMLHDASTIAAVIVEPLAGSTGVLVPPQGYLQRLRQICDKHGILLIF 244 Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG---- 317 DEVI G GR G F SQY+G PDLM +AKG+ + +PMG V R I + + G Sbjct: 245 DEVITGLGRLGAPFASQYFGVTPDLMTLAKGINNATVPMGAVAARQSIHDTIVNAGQAGA 304 Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376 EF+HG+TYSGHP+AAA A + + R E + + A+ AP+ + L P V + R Sbjct: 305 IEFFHGYTYSGHPLAAAAACAALDLYRSEDLFNRA-AQMAPHFEDAIHALKGLPGVLDIR 363 Query: 377 GVGMVAALEL-----VKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVI 431 +G+V +EL + E F CF G+++R GD + SPPL++ Sbjct: 364 NLGLVGGVELQPRAGAPGARAHEIFV----------KCFEQGVLIRYTGDILAFSPPLIV 413 Query: 432 DPSQIDELITLARKCLDQTA 451 D +QI +L + + + TA Sbjct: 414 DQAQIAQLFDVVAQAIRTTA 433 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: 536 Number of extensions: 33 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: 456 Length of database: 433 Length adjustment: 32 Effective length of query: 424 Effective length of database: 401 Effective search space: 170024 Effective search space used: 170024 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