Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF2981 HP15_2925 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Marino:GFF2981 Length = 450 Score = 225 bits (574), Expect = 2e-63 Identities = 132/415 (31%), Positives = 217/415 (52%), Gaps = 7/415 (1%) Query: 39 ITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPP 98 I + EGV++ D EGN+ +DA++ W G+ + A +Q+ EL L T H P Sbjct: 33 IKRGEGVWLEDFEGNRFIDAVSSWWVNLFGHANPRINAAIQKQIGELEHVILAGFT-HEP 91 Query: 99 VVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHG 158 VV L++ + +V P G+N VF+ +GS A + L+M HYW +P KK + N YHG Sbjct: 92 VVNLSERLIEVTPPGLNKVFYADNGSSAIEAALKMSFHYWKNHDKPGKKNFVNLSNSYHG 151 Query: 159 STVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEV 218 T+ ++LG + + + ++ P + + + +++ + E +EK + E Sbjct: 152 ETLGALALGDVSLYKDTYQPLLMEVLTAPSPDAFNKEPGETDEDYALRQFEAMEKLLAEK 211 Query: 219 GEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQ 278 EE A + IQ AGG+ + Y K+RE +Y + IADE+ GFGRTG F + Sbjct: 212 HEEICAVVVEPLIQCAGGMRMHHPIYHTKLREACDRYGVHLIADEIAVGFGRTGTLFACE 271 Query: 279 YYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGE----FYHGFTYSGHPVAAAV 334 G PD M ++KGLT+GY+P+ V+ D++ E F H +Y+G+P+ AV Sbjct: 272 QSGITPDFMCLSKGLTAGYLPLSVVLTTDDVYNAFYDDYETLKAFLHSHSYTGNPIGCAV 331 Query: 335 ALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKKTRE 394 AL + I R++ +IE +A + + + LADHP VG+ R GM A+E+VK+K ++ Sbjct: 332 ALATLDIFRDDNVIESNRA-LSTCMAESVAHLADHPNVGDIRQHGMTLAVEMVKDKASKT 390 Query: 395 RFT-DKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQIDELITLARKCLD 448 F + G+ +H ++R +G+ + PP VI QI L +A + ++ Sbjct: 391 PFPWQERRGIRVYQHALTRQALLRPLGNVVYFMPPYVITEEQIRHLAQVATEGIE 445 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: 540 Number of extensions: 28 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: 450 Length adjustment: 33 Effective length of query: 423 Effective length of database: 417 Effective search space: 176391 Effective search space used: 176391 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