Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Dino:3607958 Length = 441 Score = 271 bits (694), Expect = 2e-77 Identities = 152/426 (35%), Positives = 233/426 (54%), Gaps = 22/426 (5%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT +Q + R+ A+G+Y +EG ++LD AGLWC N G+ R +V+A Q Sbjct: 18 PFTANRQF-KSNPRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAA 76 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 EL Y FQ HP ELA + ++AP+GM+HVF+T SGSEA ++ L++ Y +G+ Sbjct: 77 ELD-YAPAFQMGHPRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGE 135 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEF 203 + +IGR GYHG G+S+GG+ + + G+ H+ + E Sbjct: 136 AGRTRLIGRERGYHGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPEL 195 Query: 204 GVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADE 263 G A+ LE+ I G E +AA I EP+ G+ GV++PP Y ++R+I + I+ I DE Sbjct: 196 GAHLADDLERIIALHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDE 255 Query: 264 VICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG----EF 319 VI GFGR G FG+Q +G PD++ AKGLT+G IPMG V+ I + QG E Sbjct: 256 VITGFGRVGAAFGAQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIEL 315 Query: 320 YHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVG 379 +HG+TYSG+P+A+A L + RE+ + + + PY Q+ L V + R +G Sbjct: 316 FHGYTYSGNPIASAAGLATLETYREDDLFARA-LDLEPYWQEALHSLKGARHVIDIRNLG 374 Query: 380 MVAALELV-----KNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPS 434 ++ A+EL K+ + F D + G+++R GD + +SPPL+I+ + Sbjct: 375 LIGAIELEPISGHPTKRAFQAFLD----------AYDKGVLIRTTGDIIALSPPLIIETA 424 Query: 435 QIDELI 440 QID ++ Sbjct: 425 QIDRIV 430 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: 570 Number of extensions: 34 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: 441 Length adjustment: 33 Effective length of query: 423 Effective length of database: 408 Effective search space: 172584 Effective search space used: 172584 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