Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate BWI76_RS27815 BWI76_RS27815 acetolactate synthase catalytic subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Koxy:BWI76_RS27815 Length = 562 Score = 252 bits (643), Expect = 3e-71 Identities = 171/473 (36%), Positives = 252/473 (53%), Gaps = 18/473 (3%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYARV 89 T Q +V LL G+ TV GIPG L +Y L S IRH+L RHEQGAGF+A G AR Sbjct: 14 TGAQLVVHLLERQGITTVSGIPGGSILPIYDALSQSTQIRHILARHEQGAGFIAQGMART 73 Query: 90 SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149 GKP VC +GPG TN+ TAI A DS+PL+ I+ ++ +G + D + Sbjct: 74 EGKPAVCMACSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTD---AFQEVDTYGI 130 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209 + PIT + L + +LP++++ A+ + S RP PV I IP DV AA + D R Sbjct: 131 SIPITKHNYLVRNIAELPQVMSDAFRIAQSGRPGPVWIDIPKDVQAATIELDALPEPGAR 190 Query: 210 PGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLL 269 S ++R AA + AA+RP+L GGG + A E + L+E+ P ++ G+L Sbjct: 191 MAAPEFDSASVREAAAMINAAQRPVLYLGGGVINAPEHIRQLAEKANLPTTQTLMALGML 250 Query: 270 PPDAPLNAG-ASLCVAPGWEMI-AEADLVLAVGTEMADTDFWR-ERLPLSGELIRVDIDP 326 P PL+ G + A I EADL++ +G D + E+ + ++I VDID Sbjct: 251 PKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGKTEQFCPNAKIIHVDIDR 310 Query: 327 RKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAE----IRAAHAPL 382 + + VA++GD + LE L+ ++ EA+ + VA L+ E I PL Sbjct: 311 SELGKIKQAHVAIQGDVGEVLEQLIPQV--EAQPRSAWLQLVADLQREFPCTIPQEQDPL 368 Query: 383 QALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAG 442 H +++ +AA + +A V+TD+ Q A+ PR WL G GT+G+GLPA Sbjct: 369 S--HYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAA 426 Query: 443 IGAKLGAPQRPGLVLVGDGGFLYTAQELATASE-ELDSPLVVLLWNNDALGQI 494 +GA L PQR + GDG + QE+ATA+E +LD + ++L NN+ALG + Sbjct: 427 VGAALANPQRKVICFSGDGSLMMNIQEMATAAENQLD--VKIILMNNEALGLV 477 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: 754 Number of extensions: 39 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: 559 Length of database: 562 Length adjustment: 36 Effective length of query: 523 Effective length of database: 526 Effective search space: 275098 Effective search space used: 275098 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