Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 209294 DVU0360 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::Q9HUI8 (559 letters) >MicrobesOnline__882:209294 Length = 563 Score = 254 bits (650), Expect = 5e-72 Identities = 179/478 (37%), Positives = 242/478 (50%), Gaps = 22/478 (4%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYAR 88 ++ + ++RLL G+D + GIPG L LY L S IRHVL RHEQGAGF+A G AR Sbjct: 4 MSGAELVIRLLERQGIDCISGIPGGANLPLYDALSHSKRIRHVLARHEQGAGFIAQGMAR 63 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 +G+P V F +GPG TN TAI A DSVP++ I+ + +G + D Sbjct: 64 STGRPAVFFATSGPGATNTLTAIADAKLDSVPVICITGQVPRSMIGSD---AFQEVDIYG 120 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHD-WSAAVA 207 M+ P+T + L S E L +I A+ + S RP PV + IP DV A VA + W Sbjct: 121 MSIPVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDIPKDVQTAEVAFEAWPETGG 180 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVAG 265 P P E L AA LA A RP+L GGG +A AGE +ER P S+ G Sbjct: 181 PDPAE-APDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLLG 239 Query: 266 KGLLPPDAPLNAG-----ASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGEL 319 G LPP+ PL G + C ++ E DL++ VG D R E+ + Sbjct: 240 LGTLPPEHPLTLGMLGMHGARCTN---MLLEECDLLMVVGARFDDRATGRIEQFCPHASI 296 Query: 320 IRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRA--EIRA 377 I VDIDP + + + VA+ GDA + LEALL L E D VAR++A + Sbjct: 297 IHVDIDPSEIDKLRTAHVAITGDAGRVLEALLPML--EPVDRKAWHGHVARMKAAHPLLT 354 Query: 378 AHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGY 437 A ++ AA L A ++TD+ Q A+ R R WL G GT+G+ Sbjct: 355 PGADDPRTPYGLVTCTAACLDDSAIIATDVGQHQMRTAQAYPLRRTRQWLTSGGLGTMGF 414 Query: 438 GLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIR 495 GLPA IGA L P+R + GDG QELATA+ E + + ++L NN+ALG ++ Sbjct: 415 GLPAAIGAALANPERTVVCFTGDGSLQMNIQELATAA-ETGANVKIVLANNNALGLVQ 471 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: 772 Number of extensions: 41 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: 563 Length adjustment: 36 Effective length of query: 523 Effective length of database: 527 Effective search space: 275621 Effective search space used: 275621 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