Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__psRCH2:GFF4212 Length = 452 Score = 799 bits (2064), Expect = 0.0 Identities = 378/451 (83%), Positives = 411/451 (91%) Query: 5 ITNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWC 64 +++++T WQALSRDHHLPPFTDYK LN KG RIITKA GVY+WDSEG+KILDAMAGLWC Sbjct: 1 MSDSQTLHWQALSRDHHLPPFTDYKALNAKGTRIITKASGVYLWDSEGHKILDAMAGLWC 60 Query: 65 VNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGS 124 VN+GYGREELV+AATRQMRELP+YNLFFQTAHPP V LAKAIAD+AP GMNHVFFTGSGS Sbjct: 61 VNLGYGREELVEAATRQMRELPYYNLFFQTAHPPAVALAKAIADIAPAGMNHVFFTGSGS 120 Query: 125 EANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIV 184 EANDTVLRMVRHYWA KGQP KKVVIGRWNGYHGST+AG SLGGMKA+HEQ D PIPGI Sbjct: 121 EANDTVLRMVRHYWAIKGQPAKKVVIGRWNGYHGSTIAGASLGGMKAMHEQSDGPIPGIE 180 Query: 185 HIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTY 244 HI QPYW+GEGGDMSP+EFGV A+QLE+KILEVGE+ VAAFIAEPIQGAGGVI+PP+TY Sbjct: 181 HIDQPYWFGEGGDMSPEEFGVRIADQLEQKILEVGEDKVAAFIAEPIQGAGGVIIPPETY 240 Query: 245 WPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVV 304 WP+I+EILA+YDILFIADEVICGFGRTGEWFGS YYG PDLMPIAKGLTSGYIPMGGV+ Sbjct: 241 WPRIKEILARYDILFIADEVICGFGRTGEWFGSDYYGLEPDLMPIAKGLTSGYIPMGGVI 300 Query: 305 VRDEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQ 364 VRDE+V+ LN+GGEFYHGFTYSGHPVAAAVALENIRILREEKI+E+VK +TAPYLQ RWQ Sbjct: 301 VRDEVVQTLNEGGEFYHGFTYSGHPVAAAVALENIRILREEKIVERVKTKTAPYLQSRWQ 360 Query: 365 ELADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMI 424 EL DHPLVGEARGVG++ ALELVKNKKTRERF D GVGMLCREHCFRNGL+MRAVGDTMI Sbjct: 361 ELLDHPLVGEARGVGLLGALELVKNKKTRERFADPGVGMLCREHCFRNGLVMRAVGDTMI 420 Query: 425 ISPPLVIDPSQIDELITLARKCLDQTAAAVL 455 ISPPLVI QIDELI R CLD TA L Sbjct: 421 ISPPLVISEEQIDELIGKVRLCLDATAKDAL 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: 847 Number of extensions: 35 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: 452 Length adjustment: 33 Effective length of query: 423 Effective length of database: 419 Effective search space: 177237 Effective search space used: 177237 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 Apr 09 2024. 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