Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_2414 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2414 Length = 472 Score = 328 bits (841), Expect = 2e-94 Identities = 169/443 (38%), Positives = 268/443 (60%), Gaps = 7/443 (1%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAAT 79 HH+ + + + E+G+ I +G YI+D++GN+ LDA+ G+WC N+G GREE+ +A Sbjct: 24 HHMHGYHVFDEHAEQGSLNIVAGDGAYIYDTQGNRFLDAVGGMWCTNIGLGREEMAEAIA 83 Query: 80 RQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWA 139 Q+R+L + N F ++ +EL + +A +AP ++HVF T GS A DT R++++Y Sbjct: 84 DQVRQLAYSNPFSDMSNNVAIELCEKLASLAPGDLDHVFLTTGGSTAVDTAYRLIQYYQN 143 Query: 140 TKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALH-EQGDFPIPGIVHIAQPYWYGEGGDM 198 +G+P+KK +I R+N YHGST +S+G A + D+ P I H++ P Y M Sbjct: 144 CRGKPEKKHIIARFNAYHGSTTLTMSIGNKAADRVPEFDYTNPLIHHVSNPNPYRAPDGM 203 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 +F + ++ E KIL +G + VA F AEPI G+GGVI+PP Y ++ ++ +YDIL Sbjct: 204 DEAQFLEFLVKEFEDKILSIGADKVAGFFAEPIMGSGGVIIPPRGYLKRMWDVCQRYDIL 263 Query: 259 FIADEVICGFGRTGEWFGS-QYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG 317 F+ADEV+ FGR G++F S + + PD++ AKGLTS Y+P+G + + I +V+ + G Sbjct: 264 FVADEVVTSFGRLGKFFASYEVFDVQPDIITTAKGLTSAYLPLGACIFSERIWKVIAEPG 323 Query: 318 E---FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGE 374 + F HGFTYSGHPV AL+NI I+ E ++ V A YL++R L D PLVG+ Sbjct: 324 KGRCFTHGFTYSGHPVCCTAALKNIEIIERENLLAHVDTVGA-YLEERLATLRDLPLVGD 382 Query: 375 ARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDP 433 R ++A +E V +K+T+ F D+ +G GL++R + ++SPPL++ Sbjct: 383 VRCQKLMACVEFVADKRTKALFPDEINIGEKIHVRAQARGLLVRPIMHLNVMSPPLILTS 442 Query: 434 SQIDELITLARKCLDQTAAAVLA 456 Q+DE++ R C+ + AA + A Sbjct: 443 VQVDEIVETLRTCILEVAAELEA 465 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: 550 Number of extensions: 27 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: 472 Length adjustment: 33 Effective length of query: 423 Effective length of database: 439 Effective search space: 185697 Effective search space used: 185697 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