Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Dsui_1925 Dsui_1925 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__PS:Dsui_1925 Length = 572 Score = 253 bits (645), Expect = 2e-71 Identities = 169/473 (35%), Positives = 238/473 (50%), Gaps = 10/473 (2%) Query: 28 KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGY 86 +TLT Q +VRLL GV TV GIPG L Y L S IRHVL RHEQGAGF+A G Sbjct: 19 ETLTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSASEKIRHVLARHEQGAGFIAQGM 78 Query: 87 ARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQ 146 AR SG+P VC +GPG TN+ TAI A DS+PL+ I+ + +G + D Sbjct: 79 ARASGQPAVCLASSGPGATNLLTAIADAKLDSIPLVAITGQVPRSMIGTD---AFQEVDT 135 Query: 147 RAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAV 206 ++ PIT + L S E+L E+I RA+ + S RP PV + IP DV A + A Sbjct: 136 YGLSIPITKHNFLVNSAEELLEVIPRAFTLAASGRPGPVLVDIPKDVQAQAIEVSQWPAP 195 Query: 207 ARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTSVA 264 R P A+ AA + AA RP+L GGG + +G EA AL+E+ + P ++ Sbjct: 196 GGRQAPPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAEKASLPTTMTLM 255 Query: 265 GKGLLPPDAPLNAGASLCVAPGWE--MIAEADLVLAVGTEMADTDFWR-ERLPLSGELIR 321 G +P D PL+ + ++ E DL++AVG D + ++I Sbjct: 256 ALGAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIH 315 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAP 381 +DIDP + + + V + GD + LE L + R R R ++ + Sbjct: 316 IDIDPSELDKIKNAHVGIAGDVGEVLEKLSPLVEAHLRKRWLTHMGDLRSRFRLQRPNLE 375 Query: 382 LQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPA 441 H ++ +A L A ++TD+ Q A+ R PR WL G GT+G+G+PA Sbjct: 376 DPRSHYGLIQAVADCLDDSAAIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPA 435 Query: 442 GIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494 +GA L P+R + GDG L QELAT + E + L ++L NNDALG + Sbjct: 436 ALGAALAEPERTVVCFTGDGSILMNIQELATIA-EAGANLKIVLMNNDALGLV 487 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: 776 Number of extensions: 44 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: 572 Length adjustment: 36 Effective length of query: 523 Effective length of database: 536 Effective search space: 280328 Effective search space used: 280328 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