Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 6939187 Sama_3281 acetolactate synthase 2 catalytic subunit (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__SB2B:6939187 Length = 556 Score = 221 bits (563), Expect = 6e-62 Identities = 173/541 (31%), Positives = 254/541 (46%), Gaps = 32/541 (5%) Query: 28 KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 87 +T+ A++++LA +GV+TVFG PG + +Y L GS + H L RHEQGAGF A GYA Sbjct: 4 QTMRGADAVIKVLAAHGVNTVFGYPGGAIMPIYDALYGSEVEHTLCRHEQGAGFAAVGYA 63 Query: 88 RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 R SGK GVCF +GPG TN+ TA+ A DSVP++ I+ ++ +G + D Sbjct: 64 RASGKTGVCFATSGPGATNLITALADALLDSVPVVAITGQVSTSVIGTD---AFQEIDVL 120 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS-AAV 206 M+ T S + + ++L + RA+ + S RP PV + IP D+ A + + AV Sbjct: 121 GMSLSCTKHSFMVQTVDELVPTLYRAFELAASGRPGPVLVDIPKDIQIAKLEYRAPLLAV 180 Query: 207 ARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTSVA 264 A P +A RA +AAA++PML GGG AG E L + P ++ Sbjct: 181 ADEPKVQDADIDAARAL---IAAAKKPMLYVGGGVGMAGAVEPLRHFIKATYMPSVATLK 237 Query: 265 GKGLLPPDAP-------LNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLS 316 G G +P P ++ G + +A + E DL++ VG D R + Sbjct: 238 GLGAIPHGTPGYLGMLGMHGGKAANLA-----VQECDLLMVVGARFDDRVTGRLASFAPN 292 Query: 317 GELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIR 376 +++ +DID + VA+ + R L L ++L D P A V L AE R Sbjct: 293 AKVLHLDIDAAELGKLRQPDVAIAAELRVVLPMLEMQL-----DIDPWRAEVEALAAEHR 347 Query: 377 --AAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGT 434 H A+L R+A LP D+ VS D+ Q R P L G GT Sbjct: 348 WDYNHPGSLIYAPAMLRRLANKLPEDSVVSCDVGQHQMWVAQHMHFRRPEDHLSSAGLGT 407 Query: 435 LGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494 +G+GLPA IGA++ P + + GDG F+ QEL T P+ +LL +N LG + Sbjct: 408 MGFGLPAAIGAQMARPDATVVAVSGDGSFMMNVQELTTIKRR-KLPVKILLIDNQRLGMV 466 Query: 495 R--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIE 552 + + + L NPDF L A+ R +E+E L G L+ Sbjct: 467 KQWQQLFFEERYSETNLSDNPDFVALASAFDIPGRTIFAAEEVEEALTEMLTSKGPYLLH 526 Query: 553 L 553 + Sbjct: 527 V 527 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: 727 Number of extensions: 37 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: 556 Length adjustment: 36 Effective length of query: 523 Effective length of database: 520 Effective search space: 271960 Effective search space used: 271960 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