Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 5208454 Shew_0966 beta alanine--pyruvate transaminase (RefSeq)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__PV4:5208454 Length = 446 Score = 301 bits (770), Expect = 4e-86 Identities = 172/436 (39%), Positives = 250/436 (57%), Gaps = 30/436 (6%) Query: 19 DHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAA 78 +H+ PFT +Q + R++ +AEG+Y D G +LD AGLWC N G+GR+ + +A Sbjct: 16 EHYWMPFTANRQFKQS-PRLLAQAEGMYYKDVNGRPVLDGTAGLWCCNAGHGRKAISEAV 74 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 ++Q+ E+ Y FQ HP ELA+ +A +AP+G+N VFFT SGSE+ DT L++ +Y Sbjct: 75 SKQIHEMD-YAPSFQMGHPLAFELAERLAAIAPKGINKVFFTNSGSESVDTALKIALNYH 133 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHE-------QGDFPIPGIVHIAQPYW 191 +G+ + IGR GYHG G+S+GG+ QG +P + I Q + Sbjct: 134 RARGEATRTRFIGRELGYHGVGFGGISVGGIGGNRRTFSQQLLQGVDHLPHTLDIQQNAF 193 Query: 192 YGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREI 251 E G AE LE+ + G EN+AA I EP+ G+ GVI+PP Y ++REI Sbjct: 194 C-----KGLPETGAEKAEVLEQLVTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREI 248 Query: 252 LAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVE 311 KY IL I DEVI GFGR G+ F SQ +G PD++ AK L +G IPMG V++ D I + Sbjct: 249 TRKYGILLIFDEVITGFGRVGDAFASQRWGVTPDMITTAKALNNGTIPMGAVLIDDAIYD 308 Query: 312 VLNQGG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELA 367 E YHG+TYSGHPVAAA A+ + I +EE++ E+ K+ Y +K L Sbjct: 309 ASMDAPEGAIELYHGYTYSGHPVAAAAAIATLDIYQEEQLFERTKS-LEGYFEKAVHSLK 367 Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGML---CREHCFRNGLIMRAVGDTMI 424 P + + R G+VA ++ +DKG+G E CF+NG ++RA DT+ Sbjct: 368 GLPNLIDIRNTGLVAGIQFSP--------SDKGIGKRGFGIFETCFKNGTLVRATADTIA 419 Query: 425 ISPPLVIDPSQIDELI 440 +SPPL++D +QID+++ Sbjct: 420 LSPPLIVDEAQIDQMV 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: 550 Number of extensions: 24 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