Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 206818 DVU1376 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::Q9HUI8 (559 letters) >MicrobesOnline__882:206818 Length = 563 Score = 223 bits (569), Expect = 1e-62 Identities = 169/545 (31%), Positives = 251/545 (46%), Gaps = 27/545 (4%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYAR 88 L Q L+ L GVD FG PG +++Y +P + HVL RHEQ A ADGYAR Sbjct: 3 LNGAQILLECLKKEGVDVFFGYPGGAVIDIYDEIPRHPELHHVLVRHEQAAVHAADGYAR 62 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 SGK GVC V +GPG TN T I AY+DS+P+++++ + +G + D Sbjct: 63 ASGKVGVCLVTSGPGATNTVTGIATAYSDSIPVVILTGQVPTPLIGND---AFQEVDIVG 119 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208 +T P T + L ++L ++ +A+ + + RP PV + +P DV+ A W V+ Sbjct: 120 ITRPCTKHNYLVRDVKELATVVRQAFYLARTGRPGPVLVDLPKDVMQAKTDFVWPEDVSM 179 Query: 209 RPGRGV--PCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVA 264 R P +R AA+ A RP+L GGG + A E L + L P+ +++ Sbjct: 180 RSYNPTYKPNLNQIRRAADAFFEAERPLLFVGGGVVMSDASEELGWFARTLRIPVASTLM 239 Query: 265 GKGLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGELIR 321 G G P D PL G + + ADL++AVG D R +I Sbjct: 240 GLGAFPGDDPLWLGMLGMHGTYAANKAVNNADLIVAVGARFDDRVTGRLSAFASKARIIH 299 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTL----EALLVRLPQEARDSAPAAARVARLRAEIRA 377 +DIDP + + GD RQ+L E L+ RL E +D A AR A R Sbjct: 300 IDIDPTSIRKNVQVGIPVVGDCRQSLANIREILVPRL--EEKDWGAAHARWLEQLASWR- 356 Query: 378 AHAPLQALH------QAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTG 431 PL Q +++++ A DA ++T++ Q + R PR+ + G Sbjct: 357 VEQPLGFSREGGIKPQQVIEQLFAITRGDAIITTEVGQNQMWTAQFYTFRKPRTLITSGG 416 Query: 432 YGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDAL 491 GT+GYG PA IGA+ P + + + GDG QELATA P+ +L+ NN L Sbjct: 417 LGTMGYGFPAAIGAQFAFPDKLVVDVAGDGSIQMNIQELATAVCN-KLPVKILILNNGYL 475 Query: 492 GQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVT 549 G +R ++ + PDF L AYG + +++ LE LR Sbjct: 476 GMVRQWQELFYQRNYCSTCMDAQPDFVKLAEAYGAEGYRITEVESLESTLREALASPHPA 535 Query: 550 LIELR 554 +I++R Sbjct: 536 IIDVR 540 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: 749 Number of extensions: 40 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