Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 3608649 Dshi_2042 aminotransferase class-III (RefSeq)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Dino:3608649 Length = 460 Score = 233 bits (593), Expect = 1e-65 Identities = 141/433 (32%), Positives = 221/433 (51%), Gaps = 22/433 (5%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78 HHL ++K RII + +G+ +WD+ G + LDA++G LW VNVGYGRE + A Sbjct: 23 HHL---INHKPFETTDPRIIVEGKGMRVWDALGKEHLDAVSGGLWTVNVGYGRERIANAV 79 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 Q+ ++ F++ T P ++ + D P GM+ V++ SGSEAN+ +MVR Sbjct: 80 RDQLMQMCFFSNSLGTI--PGAIFSEMLIDKMP-GMSRVYYASSGSEANEKAFKMVRQIA 136 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM 198 +K ++ R YHGST+A +S GG Q P V + P+ Sbjct: 137 HKVHGGRKTKILYRERDYHGSTLATMSAGGQWERKAQYGPFAPDFVEV--PHCLEYRAQW 194 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 + +G AA+ +E+ IL G + V A EP+ GGVI PP+ YWP+++EI KYD+L Sbjct: 195 EGENYGERAADAIEEVILREGPDTVGALCLEPVTAGGGVITPPEGYWPRVQEICRKYDVL 254 Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG-- 316 DEV+CG GRTG+WFG Q+YG PD + +AKG+ SGY + +V + + E+ Sbjct: 255 LHIDEVVCGLGRTGKWFGYQHYGIEPDFVTMAKGVASGYAAISCMVTTERVFEMFKSEPG 314 Query: 317 ---GEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVG 373 F T+ G A A+EN++I+ EE ++ + + H ++G Sbjct: 315 APLDYFRDISTFGGCTAGPAAAIENMKIIEEEDLLGNTDRMHDQLMGNLAGLMEKHRVIG 374 Query: 374 EARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAV-------GDTMIIS 426 + RG G+ ELV ++ T+E + V + + C G+I+ A +T+ S Sbjct: 375 DIRGKGLFCGAELVADRTTKEPAPEALVQAVVAD-CMAQGVIIGATNRSLPGYNNTLCFS 433 Query: 427 PPLVIDPSQIDEL 439 P L+ ID++ Sbjct: 434 PALIATADDIDQI 446 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: 625 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 456 Length of database: 460 Length adjustment: 33 Effective length of query: 423 Effective length of database: 427 Effective search space: 180621 Effective search space used: 180621 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