Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PP_2588 PP_2588 Aminotransferase, class III
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Putida:PP_2588 Length = 460 Score = 499 bits (1284), Expect = e-145 Identities = 235/449 (52%), Positives = 321/449 (71%), Gaps = 4/449 (0%) Query: 9 KTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVG 68 +TR++QA HH+ F D K LN +G R+I E +++WDSEG + LD M+GLWC +G Sbjct: 10 QTRDYQAADAAHHIHAFLDQKALNAEGPRVIVGGERLHLWDSEGKRYLDGMSGLWCTQLG 69 Query: 69 YGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEAND 128 YGR +L AA QM +L +YN+FF T HP V+EL++ + + P +H +T SGSEAN+ Sbjct: 70 YGRRDLTAAAATQMDQLAYYNMFFHTTHPAVIELSELLFSLLPGHYSHAIYTNSGSEANE 129 Query: 129 TVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQ 188 ++R VR YW GQP KK++IGRWNGYHGST+A +LGGMK +H+ G IP + HI + Sbjct: 130 VLIRTVRRYWQVVGQPGKKIMIGRWNGYHGSTLAATALGGMKFMHDMGGL-IPDVAHIDE 188 Query: 189 PYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKI 248 PYWY EGG+++P EFG A QLE+KILE+G ENVA FIAEP QGAGG+I PP++YWP+I Sbjct: 189 PYWYAEGGELTPAEFGRRCALQLEEKILELGAENVAGFIAEPFQGAGGMIFPPESYWPEI 248 Query: 249 REILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDE 308 + I +YD+L ADEVI GFGRTGEWF +Y+G PD + IAKGLTSGY+PMGG+V+ Sbjct: 249 QRICRQYDVLLCADEVIGGFGRTGEWFAHEYFGFEPDTLSIAKGLTSGYVPMGGLVLSKR 308 Query: 309 IVEVL-NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL- 366 I E L +GG F HG TYSGHPVAAAVA+ N++ LR+E I+ +VK +T PYLQ+ +E+ Sbjct: 309 IAEALVERGGVFAHGLTYSGHPVAAAVAIANLKALRDEGIVRQVKDDTGPYLQRILREVF 368 Query: 367 ADHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMII 425 ADHPL+G+ +G G+VAAL+ ++K TR+RF ++ + CR F G+I+R+ MI+ Sbjct: 369 ADHPLIGQVQGAGLVAALQFAEHKPTRKRFANENDLAWQCRTFGFEEGVIIRSTLGRMIM 428 Query: 426 SPPLVIDPSQIDELITLARKCLDQTAAAV 454 +P L+ + S++DEL+ R +D+TA V Sbjct: 429 APALIANHSELDELVEKTRIAVDRTARLV 457 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: 696 Number of extensions: 40 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: 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