Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 5207768 Shew_0289 acetolactate synthase 2 catalytic subunit (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__PV4:5207768 Length = 557 Score = 229 bits (585), Expect = 2e-64 Identities = 180/546 (32%), Positives = 261/546 (47%), Gaps = 32/546 (5%) Query: 24 MQPQKTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMA 83 M+ + + A+++ LA +GV TVFG PG + +Y L G+ + H+L+RHEQGA F A Sbjct: 1 MEQGQKIRGADAVIKALAAHGVTTVFGYPGGAIMPIYDALVGAPVEHLLSRHEQGAAFAA 60 Query: 84 DGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHET 143 GYAR SGK GVCF +GPG TN+ T + A DSVPL+ I+ +A +G + Sbjct: 61 VGYARASGKTGVCFATSGPGATNLVTVLADALLDSVPLVAITGQVSTAVIGTD---AFQE 117 Query: 144 QDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS 203 D M+ T S + E+L + RA+ + S RP PV + IP D+ A + D+ Sbjct: 118 IDVLGMSLSCTKHSFMVTDVEELVPTLYRAFEIAASGRPGPVLVDIPKDIQIALL--DYK 175 Query: 204 AAV-ARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLF 260 A + A +P V S L +A +A A+RPML GGG AG E L + P Sbjct: 176 APLQAIQPEPQVDPS-LLESAKNLIAQAQRPMLYVGGGVGMAGAVEQLRDFINQSGMPSV 234 Query: 261 TSVAGKGLLPPDAP-------LNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ER 312 ++ G G + D P ++ G + +A + E DL+L VG D R Sbjct: 235 ATLKGLGSIAHDHPGYLGMLGMHGGKAANLA-----VQECDLLLVVGARFDDRVTGRLAS 289 Query: 313 LPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLR 372 +++ +DID + VA+ GD R+ L AL L + AP A VARL+ Sbjct: 290 FAEHAKVVHLDIDIAELGKLRRPDVAIAGDLREILPALAQPL-----EIAPWLAEVARLK 344 Query: 373 AEIRAAHAPLQALHQA--ILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPT 430 A+ ++ L A +L+R+AA LP D+ V+ D+ Q R P L Sbjct: 345 AQHAWSYDRPGELIFAPKLLNRLAAKLPEDSVVACDVGQHQMWVAQHMWFRRPEDHLSSA 404 Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490 G GT+G+GLPA IGAK+ P + + GDG F+ QEL T PL +LL +N Sbjct: 405 GLGTMGFGLPAAIGAKVARPDACVVAVSGDGSFMMNVQELTTIKRR-QIPLKILLIDNQK 463 Query: 491 LGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGV 548 LG ++ + + L NPDF + A+ R E+E L G Sbjct: 464 LGMVKQWQQLFFEERFSETDLSDNPDFVTMASAFDIPGRTITQAGEVESALDEMLDAKGP 523 Query: 549 TLIELR 554 L+ +R Sbjct: 524 FLLHVR 529 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: 750 Number of extensions: 55 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: 557 Length adjustment: 36 Effective length of query: 523 Effective length of database: 521 Effective search space: 272483 Effective search space used: 272483 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