Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO353_08585 AO353_08585 aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08585 Length = 454 Score = 753 bits (1943), Expect = 0.0 Identities = 350/448 (78%), Positives = 402/448 (89%) Query: 7 NAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66 N +TREWQ LS +HHL PF+D+KQL EKG RIIT A+GVY+WDSEGNKILD MAGLWCV Sbjct: 5 NPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVA 64 Query: 67 VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126 +GYGR+EL AA++QMRELP+YNLFFQTAHPPV+ELAKAI+D+APEGMNHVFFTGSGSE Sbjct: 65 IGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEG 124 Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186 NDT+LRMVRHYWA KGQP KKV+I R NGYHGSTVAG SLGGM +HEQGD PIPGIVHI Sbjct: 125 NDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184 Query: 187 AQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWP 246 QPYW+GEGGDM+P+EFG+WAA QLE+KILE+G + V AFIAEPIQGAGGVI+PPD+YWP Sbjct: 185 PQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244 Query: 247 KIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVR 306 +I+EILAKYDILF+ADEVICGFGRTGEWFGS +YG PD+M IAKGLTSGYIPMGG++VR Sbjct: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304 Query: 307 DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL 366 DE+VEVLN+GG+F HGFTYSGHPVAAAVALENIRILREEKIIE V+AETAPYLQKR +EL Sbjct: 305 DEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLREL 364 Query: 367 ADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIIS 426 DHPLVGE RGVG++ A+ELV++K TR R+ KGVGM+CR+ CF NGLIMRAVGDTMII+ Sbjct: 365 NDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIA 424 Query: 427 PPLVIDPSQIDELITLARKCLDQTAAAV 454 PPLVI ++IDEL+T ARKCLD T +A+ Sbjct: 425 PPLVITKAEIDELVTKARKCLDLTLSAL 452 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: 838 Number of extensions: 42 Number of successful extensions: 1 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 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