Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate SMc01534 SMc01534 omega amino acid--pyruvate transaminase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Smeli:SMc01534 Length = 442 Score = 291 bits (744), Expect = 4e-83 Identities = 168/431 (38%), Positives = 239/431 (55%), Gaps = 17/431 (3%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT +Q +K R+ A+ +Y +G +LD AGLWCVN G+ R ++ +A Q Sbjct: 18 PFTANRQF-KKEPRLFVGAKDMYYTTHDGRTVLDGTAGLWCVNAGHCRPKITEAIREQAG 76 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 EL Y FQ HP ELA + D+APEGMNHV +T SGSE+ DT L++ Y KG Sbjct: 77 ELD-YAPAFQLGHPKAFELANRLVDIAPEGMNHVLYTNSGSESVDTALKVALAYHRAKGN 135 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGG-DMSPDE 202 + +IGR GYHG G+S+GG+ A + + G+ H+ + + E Sbjct: 136 GSRFRLIGRERGYHGVNFGGISVGGIVANRKMFGTLLTGVDHLPHTHLPAKNAFSRGEPE 195 Query: 203 FGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIAD 262 G A +LE+ + VAA I EP+ G+ GV++PP Y K+REI K+ IL I D Sbjct: 196 HGADLAAELERIVTLHDASTVAAVIVEPVAGSTGVLIPPKGYLQKLREICTKHGILLIFD 255 Query: 263 EVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG----E 318 EVI G+GR G F +QY+ PD++ AKGLT+G IPMG V V EI + G E Sbjct: 256 EVITGYGRLGTPFAAQYFDVKPDIITTAKGLTNGVIPMGAVFVTSEIHDAFMTGPEHLIE 315 Query: 319 FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGV 378 F+HG+TYSG+P+A+A AL + REE ++ + AE APY ++ L D P V + R + Sbjct: 316 FFHGYTYSGNPIASAAALGTLDTYREEGLLTRA-AELAPYWEEALHSLKDCPHVIDIRNI 374 Query: 379 GMVAALEL--VKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436 G++ A+EL + + T+ F+ + GL++R GD + +SPPL+I+ QI Sbjct: 375 GLIGAVELEPIAGEPTKRAFS-------AFLKAYEKGLLIRTTGDIIALSPPLIIEKRQI 427 Query: 437 DELITLARKCL 447 DEL R L Sbjct: 428 DELFDKLRDVL 438 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: 535 Number of extensions: 36 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: 442 Length adjustment: 33 Effective length of query: 423 Effective length of database: 409 Effective search space: 173007 Effective search space used: 173007 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