Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 351605 BT2077 acetolactate synthase large subunit (NCBI ptt file)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Btheta:351605 Length = 565 Score = 199 bits (507), Expect = 2e-55 Identities = 163/539 (30%), Positives = 244/539 (45%), Gaps = 21/539 (3%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPG--SGIRHVLTRHEQGAGFMADGYA 87 +T +A++R L + GV T+FG PG + + L + + H+L RHEQGA A GYA Sbjct: 6 ITGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYDHQNTLNHILVRHEQGAAHAAQGYA 65 Query: 88 RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 RVSGK GVC V +GPG TN T I A DS P++VI+ + LG + D Sbjct: 66 RVSGKVGVCLVTSGPGATNTITGIADAMIDSTPIVVIAGQVGTGFLGTD---AFQEVDLV 122 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 +T PI +S E + IARA+ + S RP PV + + ++ + Sbjct: 123 GITQPIAKWSYQIRRAEDVAWAIARAFYIASSGRPGPVVLDFAKNAQVEKTKYEPTKQEF 182 Query: 208 RRPGRGVPCS--EALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTSV 263 R VP + E+++AAAE + A RP+++ G G +A E L E+ P ++ Sbjct: 183 IRSYVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKADMPAGCTL 242 Query: 264 AGKGLLPPDAPLNAGASLC---VAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGEL 319 G LP D PLN G + P + D+++AVG D ++ Sbjct: 243 LGLSALPTDHPLNKGMLGMHGNLGPNIN-TNKCDVLIAVGMRFDDRVTGNLATYAKQAKV 301 Query: 320 IRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQ----EARDSAPAAARVARLRAEI 375 I DIDP + N +A+ GD ++TL A+ L + E DS V + Sbjct: 302 IHFDIDPAEVNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTEWVDSFKEYEAVEEEKVIR 361 Query: 376 RAAHAPLQALHQA-ILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGT 434 H +L ++ ++ A +A + TD+ Q F RS + G GT Sbjct: 362 PELHPATDSLSMGEVVRAVSEATRHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGT 421 Query: 435 LGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494 +G+GLPA IGA G P R V +GDGG QEL T E+ +P+ ++ NN+ LG + Sbjct: 422 MGFGLPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTIMEQ-KAPVKIICLNNNYLGNV 480 Query: 495 RDDMLGLDIEPVGVLPR-NPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIE 552 R P NPD+ + AY ++ +EL+ + G L+E Sbjct: 481 RQWQAMFFNRRYSFTPMLNPDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDGAFLLE 539 Lambda K H 0.321 0.136 0.412 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: 663 Number of extensions: 34 Number of successful extensions: 7 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: 559 Length of database: 565 Length adjustment: 36 Effective length of query: 523 Effective length of database: 529 Effective search space: 276667 Effective search space used: 276667 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: 53 (25.0 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