Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate RR42_RS01575 RR42_RS01575 omega amino acid--pyruvate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Cup4G11:RR42_RS01575 Length = 443 Score = 255 bits (651), Expect = 2e-72 Identities = 160/439 (36%), Positives = 236/439 (53%), Gaps = 27/439 (6%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT +Q + R++ A G+Y +G +ILD AGLWCV G+ R+E+ A RQ++ Sbjct: 17 PFTANRQY-KAAPRLLDSASGMYYTSHDGRQILDGCAGLWCVAAGHCRQEIADAVARQVQ 75 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 L Y FQ +HP E A +A + P G++ +FFT SGSE+ DT L++ Y +G+ Sbjct: 76 TLD-YAPPFQMSHPLTFEAATKVAAIMPAGLDRIFFTNSGSESVDTALKIALAYHRARGE 134 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGM----KALHEQ---GDFPIPGIVHIAQPYWYGEGG 196 Q+ VIGR GYHG G+++GG+ KA G +P ++IA+ Y +G Sbjct: 135 GQRTRVIGRERGYHGVGFGGMAVGGIGPNRKAFSANLMPGTDHLPATLNIAEAA-YSKG- 192 Query: 197 DMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYD 256 +G A+ LE+ + NVAA I EP+ G+ GV+VPP Y K+REI +K+ Sbjct: 193 ---QPTWGAHLADDLERILALHDPSNVAAVIVEPLAGSAGVLVPPVGYLEKLREITSKHG 249 Query: 257 ILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVE-VLNQ 315 IL I DEVI FGR G ++ + PDL+ +AK + + +PMG V VR E+ + V+N Sbjct: 250 ILLIFDEVITAFGRLGAATAAERFNVTPDLITMAKAINNAAVPMGAVAVRREVHDTVVNA 309 Query: 316 GG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPL 371 EF HG+TYSGHP+A A A+ + I + E + + AE AP + + P Sbjct: 310 AAPGAIEFLHGYTYSGHPLAMAAAIATLDIYKNENLFGRA-AELAPKFEAAVHAVRGAPH 368 Query: 372 VGEARGVGMVAALELVKNKKTRERFTDKGV-GMLCREHCFRNGLIMRAVGDTMIISPPLV 430 V + R +GMVA +EL R G G C G+++R GD + SPPL+ Sbjct: 369 VKDIRNLGMVAGIEL------EPRPGQPGARGYEAFLKCLERGVLVRYTGDILAFSPPLI 422 Query: 431 IDPSQIDELITLARKCLDQ 449 I +QI+E+ + L + Sbjct: 423 ITEAQIEEMFDTVKTVLQE 441 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: 548 Number of extensions: 29 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: 443 Length adjustment: 33 Effective length of query: 423 Effective length of database: 410 Effective search space: 173430 Effective search space used: 173430 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