Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate WP_057509298.1 ABB28_RS14475 acetolactate synthase 2 catalytic subunit
Query= SwissProt::Q9HUI8 (559 letters) >NCBI__GCF_001431535.1:WP_057509298.1 Length = 578 Score = 233 bits (593), Expect = 2e-65 Identities = 169/543 (31%), Positives = 261/543 (48%), Gaps = 17/543 (3%) Query: 22 LPMQPQKTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGF 81 +P Q + L + L GV T+FG PG + Y L S ++HVL RHEQGA Sbjct: 3 IPAQRSAPPNGARWLTQALEAEGVQTLFGYPGGTIMPFYDALVDSRLKHVLVRHEQGAAL 62 Query: 82 MADGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLH 141 A+G+AR SG+ GVC +GPG +N+ T I A DSVP++ I+ + LG Sbjct: 63 AANGFARASGRVGVCIATSGPGASNLVTGIADAMLDSVPMVCITGQVATPLLGTD---AF 119 Query: 142 ETQDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHD 201 + D +T PI S L S + LP ++A A+ + RP PV I +P DV A +H Sbjct: 120 QELDVFGLTLPIVKHSWLVRSVDDLPRVVAEAFRIAREGRPGPVLIDLPKDVQVADASHL 179 Query: 202 WSAAVARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAA---P 258 + A P +A+ A +A A +P++ AGGG +A G+A+ AL + AA P Sbjct: 180 PAHVPATVEAPPAPAEQAIADAIAAIAGAEKPVIYAGGG-IALGDAVDALRDFAAASGIP 238 Query: 259 LFTSVAGKGLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMAD--TDFWRERLP 314 ++ G G LP P + G + EADL+L +G D T E P Sbjct: 239 AVLTLRGLGALPAGHPQSLGMLGMHGTRAANMAVQEADLLLVLGARFDDRATGKLTEFAP 298 Query: 315 LSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAE 374 + ++ +D D + + + VA+ G+ Q + AL P A R A+ R + Sbjct: 299 FA-RVVHIDADAYEISKLRTADVAVPGNVAQAIRALHAAFPAPPATQAAWRNRCAQHREK 357 Query: 375 IRAAH-APLQALH-QAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGY 432 A + AP + ++ A+L R++ PADA ++ D+ Q PR+ L Sbjct: 358 FIARYDAPGKHIYAPALLKRLSELAPADAVIACDVGQHQMWVAQHCRFNHPRNHLTSGAL 417 Query: 433 GTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALG 492 GT+G+GLPA +GA+ P R +++ GDG F+ QEL T + P+ ++L +N +LG Sbjct: 418 GTMGFGLPAAMGAQFACPDRTVVLVSGDGSFMMNVQELTTIA-RCRLPVKIVLLDNSSLG 476 Query: 493 QIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTL 550 +R ++ + L NPDF L + +G A + D++E L A + G L Sbjct: 477 MVRQWQELFFAERYSEIDLSDNPDFVALAKVFGIAATRIDARDDVEGGLAALLAEPGPAL 536 Query: 551 IEL 553 + + Sbjct: 537 LHV 539 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: 762 Number of extensions: 46 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: 578 Length adjustment: 36 Effective length of query: 523 Effective length of database: 542 Effective search space: 283466 Effective search space used: 283466 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 24 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