Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 17731 b3671 acetolactate synthase large subunit (NCBI)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Keio:17731 Length = 562 Score = 247 bits (631), Expect = 8e-70 Identities = 168/477 (35%), Positives = 247/477 (51%), Gaps = 18/477 (3%) Query: 27 QKTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADG 85 +K T + +V L G+ V GIPG L +Y L S IRH+L RHEQGAGF+A G Sbjct: 10 RKRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQG 69 Query: 86 YARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQD 145 AR GKP VC +GPG TN+ TAI A DS+PL+ I+ ++ +G + D Sbjct: 70 MARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD---AFQEVD 126 Query: 146 QRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAA 205 ++ PIT + L E+LP++++ A+ + S RP PV I IP DV A + A Sbjct: 127 TYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPA 186 Query: 206 VARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAG 265 +A + E++R AA + AA+RP+L GGG + A + L+E+ P ++ Sbjct: 187 MAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMA 246 Query: 266 KGLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGELIRV 322 G+LP PL+ G V ++ EADL++ +G D + E+ + ++I V Sbjct: 247 LGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHV 306 Query: 323 DIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAE----IRAA 378 DID + VA++ D L L+ + EA+ A VA L+ E I A Sbjct: 307 DIDRAELGKIKQPHVAIQADVDDVLAQLIPLV--EAQPRAEWHQLVADLQREFPCPIPKA 364 Query: 379 HAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYG 438 PL H +++ +AA + +A ++TD+ Q A+ PR WL G GT+G+G Sbjct: 365 CDPLS--HYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFG 422 Query: 439 LPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASE-ELDSPLVVLLWNNDALGQI 494 LPA IGA L P R L GDG + QE+ATASE +LD + ++L NN+ALG + Sbjct: 423 LPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLD--VKIILMNNEALGLV 477 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: 752 Number of extensions: 39 Number of successful extensions: 3 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: 562 Length adjustment: 36 Effective length of query: 523 Effective length of database: 526 Effective search space: 275098 Effective search space used: 275098 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