Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate H281DRAFT_03007 H281DRAFT_03007 acetolactate synthase-1/2/3 large subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Burk376:H281DRAFT_03007 Length = 587 Score = 175 bits (444), Expect = 4e-48 Identities = 147/485 (30%), Positives = 219/485 (45%), Gaps = 30/485 (6%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARV 89 ++ G + + L N GVDT+F + G H +++Y G GIR + RHEQ A ADGYAR Sbjct: 31 VSGGHLVAKALKNEGVDTIFTLCGGHIIDIYDGCVDEGIRIIDVRHEQVAAHAADGYARQ 90 Query: 90 SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149 +GK G GPG TN T I A+ P+L I A G L + M Sbjct: 91 TGKLGCVVTTAGPGCTNAVTGIATAFRSESPILHIG--GQGALTQHKMGSLQDLPHVDIM 148 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209 APIT F+A S E++ ++I+ A + P P ++ IP DVL V D S AV + Sbjct: 149 -APITKFAASVSSTERVADMISMAARECFNGAPGPAYLEIPRDVLDREV--DLSRAVVPQ 205 Query: 210 PG------RGVPCSEALRAAAERLAAARRPMLIAGGGALAA--GEALAALSERLAAPLFT 261 PG + + + A+ L + RP ++ G A E AL L P + Sbjct: 206 PGHYRASTKSIGDPRDIEKLADILVNSERPAILYGQQVWTARGHEEAIALLRGLDIPGYF 265 Query: 262 SVAGKGLLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIR 321 + A +GLLPP P + + A A AD+++ VGT + +R+ L++ Sbjct: 266 NGASRGLLPPGDPHHFDRTRSQA-----FANADVLIVVGTPFDFRMGYGKRISKELTLVQ 320 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAAR--VARLR-AEIRAA 378 +D+D R + L GD L A+L +D A R +A+L+ AE A Sbjct: 321 IDMDYRTVGKNRDIDLGLVGDPGAILAAVLQAASGRLKDDKRQARRKWMAQLQDAEATAT 380 Query: 379 H--APLQALHQAILDRIAAALPADAFVSTDMTQLAYTGN------YAFASRAPRSWLHPT 430 PL + + A + F++ D + G+ A R P W+ P Sbjct: 381 EKLMPLFKSNSTPIHPYRVAYELNEFLADDTVYIGDGGDVVTISAQAVRPRRPGQWMDPG 440 Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490 G+LG G + AK+ PQ+ L GDG F TA ++ TA+ +P + ++ NN A Sbjct: 441 ALGSLGVGTGFALAAKIAHPQKEVLCYYGDGSFGMTAFDMETAN-RFGAPYLAVIGNNSA 499 Query: 491 LGQIR 495 + QIR Sbjct: 500 MNQIR 504 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: 779 Number of extensions: 50 Number of successful extensions: 6 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: 587 Length adjustment: 36 Effective length of query: 523 Effective length of database: 551 Effective search space: 288173 Effective search space used: 288173 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