Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 226 bits (577), Expect = 9e-64 Identities = 143/440 (32%), Positives = 220/440 (50%), Gaps = 19/440 (4%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78 HHL ++ KG I+ + EG+ + D G + LDA +G +WCVNVGYGRE + +A Sbjct: 22 HHL---VQHQAFAGKGPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAV 78 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 QM+ +P+Y + P +E A+ + P G+ + + SGSEAN+ +MVR Sbjct: 79 YEQMKAMPYYAA--TAGNIPYIEFAQKLLAHMP-GLTRAYLSNSGSEANEKAYKMVRSLA 135 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM 198 G P KK ++ R YHG+T+ +S G E +PG V Y + Sbjct: 136 HLSGNPAKKKILFRARDYHGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNK 195 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 + + A +E+ I + G E V I EPI GGVI P Y+ + +I ++ +L Sbjct: 196 TYPGCDIDCARAVERIIEQEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVL 255 Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEV-LNQGG 317 I DEV+CG GRTG FG Q+YG PD++ +AKG+ S Y+P+ +E+ + LN Sbjct: 256 LIMDEVVCGMGRTGTMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPA 315 Query: 318 E----FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVG 373 + F TY G + ALEN+ I+ EEK+++ V A YL +EL D P VG Sbjct: 316 DKMAYFRDISTYGGCAAGCSAALENMAIIEEEKLLDNVNA-MGDYLLAGLKELGDLPYVG 374 Query: 374 EARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMR------AVGDTMIISP 427 + RG G++ +ELV++K ++ + V + E L+ R + + I+P Sbjct: 375 DVRGKGLLCGIELVQDKAGKKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAP 434 Query: 428 PLVIDPSQIDELITLARKCL 447 V+ ID ++ R L Sbjct: 435 AYVVTRDNIDVILRTLRAAL 454 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: 563 Number of extensions: 35 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: 459 Length adjustment: 33 Effective length of query: 423 Effective length of database: 426 Effective search space: 180198 Effective search space used: 180198 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