Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 8501148 DvMF_1883 acetolactate synthase catalytic subunit (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Miya:8501148 Length = 615 Score = 239 bits (609), Expect = 3e-67 Identities = 188/533 (35%), Positives = 250/533 (46%), Gaps = 28/533 (5%) Query: 26 PQKTLTAGQALV-RLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMA 83 P+K G LV RLL G+D + GIPG L LY L +G IRHVL RHEQGAGFMA Sbjct: 21 PRKRQPNGADLVIRLLERQGIDVIAGIPGGANLPLYDALGRAGSIRHVLARHEQGAGFMA 80 Query: 84 DGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHET 143 G ARV+G+P V F +GPG TN TAI A DSVP++ I+ LG + Sbjct: 81 QGMARVTGRPAVFFATSGPGATNTLTAIADAKLDSVPVVCITG---QVPLGLVGSDAFQE 137 Query: 144 QDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS 203 D M+ P+T + L S E+L E+I A+ + S RP PV + IP +V A V Sbjct: 138 VDIYGMSIPVTKHNFLVRSVEELAEVIPAAFRIAASGRPGPVLVDIPKNVQMAEVD---Q 194 Query: 204 AAVARRPGRGVPCS------EALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERL 255 A P G P + + AA L AA+RPML GGG +A+G + L+ER Sbjct: 195 AVFDNPPQPGQPAAPPAPDPAGISRAAALLNAAQRPMLYLGGGVVASGASDMAVQLAERA 254 Query: 256 AAPLFTSVAGKGLLPPDAPLNAGASLCVAPGWE--MIAEADLVLAVGTEMADTDFWR-ER 312 P ++ G +P PL+ G A ++AE D++L G D + ER Sbjct: 255 GLPTVMTLMALGAMPAGHPLSLGMLGMHAARHTNLLLAECDVLLVAGARFDDRAVGKAER 314 Query: 313 LPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEA---RDSAPAAARVA 369 +I +DID + + P + GD L LL L A R++ Sbjct: 315 FCPGATIIHIDIDESELDKILPVHCGITGDVGLALAELLPLLRTRAEAGREAWLTRVEEC 374 Query: 370 RLRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHP 429 R R A ++ A A+ DA V+TD+ Q A+ R PR WL Sbjct: 375 RRRHPFVMPGADDPRTPYGLIRCAADAVDHDAIVATDVGQHQMRTAQAYPLRGPRRWLTS 434 Query: 430 TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNND 489 G GT+G+GLPA IGA L P+ L GDG QELATA+EE + +LL +N+ Sbjct: 435 GGLGTMGFGLPAAIGAALARPEATVLCFTGDGSLQMNIQELATAAEE-GVNVKILLADNN 493 Query: 490 ALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLR 540 ALG +R ++ R DFA + +G DLD E LR Sbjct: 494 ALGLVRQQQELFYEGRLVASTYRRKVDFARIAEGFGVPA---VDLDASEHPLR 543 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: 976 Number of extensions: 61 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 559 Length of database: 615 Length adjustment: 37 Effective length of query: 522 Effective length of database: 578 Effective search space: 301716 Effective search space used: 301716 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