Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Ga0059261_0285 Ga0059261_0285 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Korea:Ga0059261_0285 Length = 552 Score = 183 bits (464), Expect = 2e-50 Identities = 175/544 (32%), Positives = 237/544 (43%), Gaps = 38/544 (6%) Query: 33 GQALVRLLANYGVDTVFGIPGVHTLELYRGLPG-SGIRHVLTRHEQGAGFMADGYARVSG 91 G+ LV L G D +F +PG L + L I V R E GA FMA ++G Sbjct: 8 GRILVDNLVAQGCDRIFHVPGESFLAVLDALHDVPEIDLVTCRQEGGAAFMACADGTMTG 67 Query: 92 KPGVCFVITGPGVTNVATAIGQAYADSVP-LLVISSVNHSASLGKGWGCLHETQDQRAMT 150 KPGVCFV GPG TN + + A DS P LL I V+ S +G+ + D AM Sbjct: 68 KPGVCFVTRGPGATNASIGVHVAMQDSQPMLLFIGDVDRSMRDREGF----QEVDFPAMF 123 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210 AP+ ++ ++PE +ARA+ V S RP PV I++P D+L D AV R Sbjct: 124 APLAKWATRIEDARRIPEYVARAWNVATSGRPGPVVIALPEDMLL-----DEVEAVDRPV 178 Query: 211 GRGVPC-----SEALRAAAERLAAARRPMLIAGGGA--LAAGEALAALSERLAAPLFTSV 263 P +A ER+ AA+RPM I GG ++ G A +ER P V Sbjct: 179 STPYPLMPDVNEDAAHQIVERIRAAKRPMAIVGGAGWDISTGRDFATFAERWGIP----V 234 Query: 264 AGKGLLPPDAPLNAGASLCVAPGW-------EMIAEADLVLAVGTEM--ADTDFWRERLP 314 AG DA N ++ G+ + I +ADL+L VG + A TD + P Sbjct: 235 AG-AFRRQDAIANTSSAWAGNLGYGPNPKLVQRIRDADLLLVVGARLGEATTDGYTLVTP 293 Query: 315 --LSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLR 372 LI V DP + N Y + +A+ D + L P + S A A L Sbjct: 294 DHPGQTLIHVHPDPEELNRVYHADMAVCCDVGIFADMLSSLKPLDTPFSGAAEAHAEWLD 353 Query: 373 -AEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTG 431 + + L Q + P DA + + + + A + L PT Sbjct: 354 WSTPKPREGVTLDLGQCVAAMRERLGPDDAIICNGAGNFSGWWHRYWHYGAQPTQLAPTS 413 Query: 432 YGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDAL 491 G +GYG PA + A L R + L GDG F+ QELATA + D+ L+VL+ +N A Sbjct: 414 -GAMGYGTPAAVAAALRLRDRLAVALAGDGDFMMNGQELATAIQH-DADLLVLIIDNGAY 471 Query: 492 GQIR-DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTL 550 G IR G NPDFA L RAYGC DE L Q+GV L Sbjct: 472 GTIRMHQEREFPARLSGTTLHNPDFAALARAYGCWAETVVKTDEFAPALDRALAQTGVRL 531 Query: 551 IELR 554 + L+ Sbjct: 532 LHLK 535 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: 782 Number of extensions: 37 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: 552 Length adjustment: 36 Effective length of query: 523 Effective length of database: 516 Effective search space: 269868 Effective search space used: 269868 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