Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate SM_b20379 SM_b20379 aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Smeli:SM_b20379 Length = 461 Score = 372 bits (955), Expect = e-107 Identities = 197/453 (43%), Positives = 280/453 (61%), Gaps = 9/453 (1%) Query: 7 NAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66 N + AL + + P+T+ E G +IT +G+Y+ D EG + ++ +AGL+C Sbjct: 2 NDRPNSLHALDKQSLVHPYTNLAVHQETGPHVITGGDGIYVVDDEGKRYIEGLAGLFCAG 61 Query: 67 VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126 +G+ + LV+AATRQ++ +PFY+ F + P + LA+ + +AP M+ VFF GSGSEA Sbjct: 62 LGFSEQRLVEAATRQLKTMPFYHSFAHKSTEPGIRLAEKLLSIAPVPMSKVFFAGSGSEA 121 Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186 NDT ++++ +Y G+P+KK +I R YHG TVA SL G+ H D PI I+H Sbjct: 122 NDTAIKLIWYYNNALGRPEKKKIISRRKAYHGVTVATASLTGLPFNHRDFDLPIANILHT 181 Query: 187 AQP-YW-YGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTY 244 P YW + E G+ + ++F A LE ILE G E +AAF AEP+ +GGVI PP TY Sbjct: 182 DCPHYWRFAETGE-TEEDFATRMANNLEAIILEEGPETIAAFFAEPVMVSGGVITPPKTY 240 Query: 245 WPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVV 304 + K++ +L KYDIL IADEVICGFGRTG FGS+ YG PD++ AK L++ Y+P+ ++ Sbjct: 241 FEKVQAVLRKYDILLIADEVICGFGRTGNMFGSETYGLKPDMISCAKQLSAAYMPISALM 300 Query: 305 VR----DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQ 360 + D +V+ + G F HGFTY GHPVAAAVALE + I E I+ V++ AP Q Sbjct: 301 INAKIADALVDQSRKIGTFSHGFTYGGHPVAAAVALEALTIYEEIDIVGHVRS-VAPAFQ 359 Query: 361 KRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAV 419 R ++L +HPL+GEARGVG+VA LE VK+K TRE F V + G++ R + Sbjct: 360 DRVRKLGEHPLIGEARGVGLVAGLEFVKDKATRENFPPAWQVANQAGKFATARGVLTRGL 419 Query: 420 GDTMIISPPLVIDPSQIDELITLARKCLDQTAA 452 GD + + P ++ID QID+L+T LD T A Sbjct: 420 GDMVSLCPAMIIDDEQIDDLMTRMGLALDDTLA 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: 564 Number of extensions: 25 Number of successful extensions: 5 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: 461 Length adjustment: 33 Effective length of query: 423 Effective length of database: 428 Effective search space: 181044 Effective search space used: 181044 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