Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 7023118 Shewana3_0356 acetolactate synthase 2 catalytic subunit (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__ANA3:7023118 Length = 557 Score = 214 bits (544), Expect = 9e-60 Identities = 172/546 (31%), Positives = 250/546 (45%), Gaps = 34/546 (6%) Query: 24 MQPQKTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMA 83 M+P + + A++++LA +GV TVFG PG + +Y L GS + H+L+RHEQGA F A Sbjct: 1 MEPGQMIRGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAA 60 Query: 84 DGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHET 143 GYAR SGK GVCF +GPG TN+ T++ A DSVP++ I+ +A +G + Sbjct: 61 VGYARASGKTGVCFATSGPGATNLITSLADALLDSVPVVAITGQVSTAVIGTD---AFQE 117 Query: 144 QDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS 203 D M+ T S + L + +A+ + S RP PV + IP D+ A + + Sbjct: 118 IDVLGMSLSCTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPKDIQIAQLEYRTP 177 Query: 204 -AAVARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTS 262 AV P +A RA LA A++PML GGG AG A+ L E + A S Sbjct: 178 LLAVTNEPQASASEIDAARAL---LAEAKQPMLYVGGGVGMAG-AVDQLREFIKATGMPS 233 Query: 263 VA---GKGLLPPDAP-------LNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-E 311 VA G G + P ++ G + +A + + DL++ G D R Sbjct: 234 VATLKGLGSIAHGTPGYLGMLGMHGGKAANLA-----VQDCDLLVVAGARFDDRVTGRLA 288 Query: 312 RLPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARL 371 ++I +DID + VA+ GD RQ AL + L + P A V L Sbjct: 289 TFANKAKVIHLDIDAAELGKLRQPDVAIAGDLRQIFPALAMAL-----NITPWQAEVEHL 343 Query: 372 --RAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHP 429 + + H A+L R+A LP D+ V D+ Q R P L Sbjct: 344 ARKHQWDYQHPGSLIYAPAMLRRLANKLPEDSVVCCDVGQHQMWVAQHMWFRRPEDHLSS 403 Query: 430 TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNND 489 G GT+G+GLPA IGA++ P + + GDG F+ QEL T P+ +LL +N Sbjct: 404 AGLGTMGFGLPAAIGAQVARPDATVVTVSGDGSFMMNVQELTTIKRR-KLPVKILLIDNQ 462 Query: 490 ALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSG 547 LG ++ + + L NPDF L A+ R DE+E L G Sbjct: 463 KLGMVKQWQQLFFEERYSETDLSDNPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKG 522 Query: 548 VTLIEL 553 L+ + Sbjct: 523 PYLLHV 528 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: 729 Number of extensions: 48 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