Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF1906 PGA1_c19360 acetolactate synthase isozyme, large subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Phaeo:GFF1906 Length = 601 Score = 199 bits (505), Expect = 3e-55 Identities = 171/566 (30%), Positives = 260/566 (45%), Gaps = 51/566 (9%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T + +V L V+ VFG+ G + + L S I + RHEQ A AD YARV+ Sbjct: 14 TVAEHIVDFLGRRNVEHVFGLCGHTNIAVLAALADSPIDFITVRHEQIASHAADAYARVT 73 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGK---GWGCLHETQDQR 147 G+ V PG+TN AT + A D VP++VI+ + GK LH Q Sbjct: 74 GRASVVLSHLSPGLTNCATGVANAALDCVPMVVIAGDIPTHYYGKHPHQEVNLHADAAQW 133 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 + P + + + E++ +A+ + +S +P PV +++P+D+ + ++ D +A Sbjct: 134 EIYRPFVKRAWRVDRADLMAEILEKAFHLAESGQPGPVLVNVPMDIFSEVISSDTFDRIA 193 Query: 208 RRPGRGVPCS---EALRAAAERLAAARRPMLIAGGGALAAGEALAALSE---RLAAPLFT 261 V S E R LAAA+ P+ GGG L A +A A + E + P+ Sbjct: 194 SNTKTLVKPSMDDETARRIVSGLAAAKDPVAYIGGGILLA-QASAEIEEFATHMGLPIAH 252 Query: 262 SVAGKGLLPPDAPLNAGASLCVAPGWEMIAE----ADLVLAVGTEM--ADTDFWRERLPL 315 S+ GKG + D PL G + G E++ + AD+V AVGT AD W Sbjct: 253 SLMGKGAVRDDHPLVMG--MTGFWGTELVNQTCLNADVVFAVGTRFKEADCSSWYPGYTF 310 Query: 316 S-------GELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAP----- 363 + ++I +DI+P++ YP+ + + DA+ L L + A+D P Sbjct: 311 NIGAKGNDTKVIHIDIEPQEIGRNYPTEIGVVADAKAALRV----LTRVAKDMYPDGFNR 366 Query: 364 --AAARVARLRAEIRAAHAPLQA------LHQAILDRIAAALPADAFVSTDMTQLAYTGN 415 A +A R + +A++ +Q + + IL ALP DA ++TD+ Sbjct: 367 TEKKAEIAAFREDFKASNVEMQTSAAFPMMPERILADTRIALPDDAIITTDVGWNKNGVG 426 Query: 416 YAFASRAPRSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASE 475 F P S L P G+ T+G+G PA IGAKL AP+R L LVGDGGF LATA Sbjct: 427 QQFDILTPGSILTPGGFATMGFGPPAAIGAKLAAPERVVLSLVGDGGFGQNPSMLATA-V 485 Query: 476 ELDSPLVVLLWNNDALGQIRDDM-------LGLDIEPVGVLPRN-PDFALLGRAYGCAVR 527 EL+ ++ L+ NN+A G I G P N P +A + RAYG Sbjct: 486 ELNLGIIWLVMNNNAFGTIAGLQKAHYGLTYGTTFPGSAAAPTNGPGYAEIARAYGAEGI 545 Query: 528 QPQDLDELERDLRAGFGQSGVTLIEL 553 + DEL L+A T++++ Sbjct: 546 RISSADELLPALQAAIASGKPTVLDV 571 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: 820 Number of extensions: 38 Number of successful extensions: 8 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: 601 Length adjustment: 36 Effective length of query: 523 Effective length of database: 565 Effective search space: 295495 Effective search space used: 295495 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