Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF3387 PGA1_c34400 aminotransferase class-III
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Phaeo:GFF3387 Length = 464 Score = 594 bits (1531), Expect = e-174 Identities = 294/453 (64%), Positives = 348/453 (76%), Gaps = 4/453 (0%) Query: 5 ITN-AKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLW 63 ITN T E QAL HH+ PFT +L EKGARIIT+A GV + DSEGN+ILDAMAGLW Sbjct: 4 ITNHLPTAELQALDAAHHMHPFTANGELAEKGARIITRARGVTLTDSEGNEILDAMAGLW 63 Query: 64 CVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSG 123 CVN+GYGR+EL A RQMRELP+YN FFQT H P + LA IA++AP+G+NHVFF GSG Sbjct: 64 CVNIGYGRDELADVAARQMRELPYYNTFFQTTHAPAIALAAKIAELAPDGLNHVFFAGSG 123 Query: 124 SEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGI 183 SEANDT +RMVRHYWA K +P K V+I R NGYHGS+V SLGGM A+HEQG PIP I Sbjct: 124 SEANDTNIRMVRHYWAMKAKPTKSVIISRKNGYHGSSVGSGSLGGMTAMHEQGGLPIPDI 183 Query: 184 VHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDT 243 HI QP W+ EGGDMS ++FG+ A++LE+ ILE+GE+ VAAFIAEP+QGAGGVIVPP T Sbjct: 184 HHINQPNWWAEGGDMSAEDFGLARAQELEQAILELGEDRVAAFIAEPVQGAGGVIVPPAT 243 Query: 244 YWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGV 303 YWP+I+ I KY+IL IADEVICGFGRTG WFGSQ G PD+M IAKGL+SGY P+GG Sbjct: 244 YWPEIQRICDKYEILLIADEVICGFGRTGNWFGSQSVGIRPDIMTIAKGLSSGYAPIGGS 303 Query: 304 VVRDEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRW 363 +V DEI V+ GEF HG+TYSGHPVAAAVALEN+RIL EE II V+ APYL+++W Sbjct: 304 IVSDEIASVIG-SGEFNHGYTYSGHPVAAAVALENLRILEEENIIGHVRDVAAPYLKEKW 362 Query: 364 QELADHPLVGEARGVGMVAALELVKNKKTRERFTDKG--VGMLCREHCFRNGLIMRAVGD 421 + LADHPLVGEA+ VGM+ ++ L NK TR F +G VG +CRE CF N L+MR VGD Sbjct: 363 EALADHPLVGEAKIVGMMGSIALTPNKATRAGFAAEGGTVGYICRERCFANNLVMRHVGD 422 Query: 422 TMIISPPLVIDPSQIDELITLARKCLDQTAAAV 454 MIISPPLVI P +ID LI AR+ LD+ AA+ Sbjct: 423 RMIISPPLVITPEEIDTLIARARQSLDECYAAL 455 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: 712 Number of extensions: 26 Number of successful extensions: 3 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: 464 Length adjustment: 33 Effective length of query: 423 Effective length of database: 431 Effective search space: 182313 Effective search space used: 182313 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