Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 203425 SO4347 acetolactate synthase II, large subunit (NCBI ptt file)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__MR1:203425 Length = 552 Score = 204 bits (519), Expect = 7e-57 Identities = 164/539 (30%), Positives = 240/539 (44%), Gaps = 32/539 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARV 89 + A++++LA +GV TVFG PG + +Y L GS + H+L+RHEQGA F A GYAR Sbjct: 2 IRGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARA 61 Query: 90 SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149 SGK GVCF +GPG TN+ T++ A DSVP++ I+ +A +G + D M Sbjct: 62 SGKTGVCFATSGPGATNLITSLADALLDSVPVVAITGQVSTAVIGTD---AFQEIDVLGM 118 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS-AAVAR 208 + T S + L + +A+ + S RP PV + IP D+ A + + AV Sbjct: 119 SLSCTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPKDIQIAHLEYRTPLLAVTN 178 Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTSVAGK 266 P + A RA LA A++PML GGG AG + L P ++ G Sbjct: 179 EPQAEMSDINAARAL---LAQAKQPMLYVGGGVGMAGAVDQLRDFINTTGMPSVATLKGL 235 Query: 267 GLLPPDAP-------LNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGE 318 G + P ++ G + +A + + DL++ G D R + Sbjct: 236 GSIAHGTPGYLGMLGMHGGKAANLA-----VQDCDLLVVAGARFDDRVTGRLATFANKAK 290 Query: 319 LIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARL--RAEIR 376 +I +DID + VA+ GD RQ AL + L + P V L + + Sbjct: 291 VIHLDIDAAELGKLRQPDVAIAGDLRQIFPALAMSL-----NITPWQVEVEHLARKHQWD 345 Query: 377 AAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLG 436 H A+L R+A LP D+ V D+ Q R P L G GT+G Sbjct: 346 YQHPGSLIYAPAMLRRLANKLPEDSVVCCDVGQHQMWVAQHMWFRRPEDHLSSAGLGTMG 405 Query: 437 YGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIR- 495 +GLPA IGA++ P + + GDG F+ QEL T P+ +LL +N LG ++ Sbjct: 406 FGLPAAIGAQVARPDATVVTVSGDGSFMMNVQELTTIKRR-KLPVKILLIDNQKLGMVKQ 464 Query: 496 -DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 + L NPDF L A+ R DE+E L G L+ + Sbjct: 465 WQQLFFEGRYSETDLSDNPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHV 523 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: 720 Number of extensions: 46 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: 552 Length adjustment: 36 Effective length of query: 523 Effective length of database: 516 Effective search space: 269868 Effective search space used: 269868 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