Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 6938546 Sama_2649 beta alanine--pyruvate transaminase (RefSeq)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__SB2B:6938546 Length = 446 Score = 311 bits (798), Expect = 2e-89 Identities = 180/439 (41%), Positives = 254/439 (57%), Gaps = 32/439 (7%) Query: 17 SRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQ 76 S +H+ PFT +Q + R++ AEG++ D +GN +LD+ AGLWC N G+GR+++ + Sbjct: 14 SLEHYWMPFTANRQF-KASPRLLASAEGMFYKDVDGNPVLDSTAGLWCCNAGHGRKKISE 72 Query: 77 AATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRH 136 A + Q+REL Y FQ HP ELA +AD+AP G+N +FFT SGSE+ DT L+M Sbjct: 73 AVSHQIRELD-YAPSFQMGHPLAFELASRLADIAPAGLNRIFFTNSGSESVDTALKMALA 131 Query: 137 YWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGM----KALHEQGDFPIPGIVHIAQPYWY 192 Y GQP + IGR GYHG G+S+GG+ + +Q + G+ H+ Sbjct: 132 YHRANGQPTRTRFIGRELGYHGVGFGGISVGGIGNNRRTFSQQ---LLQGVDHLPHTL-- 186 Query: 193 GEGGDMSPDEF-------GVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYW 245 D++ + F G+ AE LE+ I G EN+AA I EP+ G+ GVI+PP Y Sbjct: 187 ----DIANNAFSRGFPAHGLEKAEVLEQLITLHGAENIAAVIVEPMSGSAGVILPPQGYL 242 Query: 246 PKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVV 305 ++R+I K+ IL I DEVI GFGR G+ F SQ +G PDLM AK L +G IPMG V V Sbjct: 243 KRLRDITKKHGILLIFDEVITGFGRVGDAFASQRWGVVPDLMTTAKALNNGAIPMGAVFV 302 Query: 306 RDEIVEVLNQGG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQK 361 ++ + G EF+HG+TYSGHPVAAA AL + I +EEK+ E+ K E Y + Sbjct: 303 SQDVHDACMTGPEELIEFFHGYTYSGHPVAAAAALATLDIYQEEKLFERTK-ELEGYWED 361 Query: 362 RWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGD 421 L D P V + R G+VA ++L N + R G E CFRNG ++R GD Sbjct: 362 AVHSLRDLPNVIDIRNTGLVAGVQLSPNDEGPGR-----RGYKVFERCFRNGTLVRVTGD 416 Query: 422 TMIISPPLVIDPSQIDELI 440 + +SPPL+++ ID+++ Sbjct: 417 IIAMSPPLIVEKQHIDQIV 435 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: 572 Number of extensions: 26 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: 446 Length adjustment: 33 Effective length of query: 423 Effective length of database: 413 Effective search space: 174699 Effective search space used: 174699 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