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_1674 Ga0059261_1674 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Korea:Ga0059261_1674 Length = 555 Score = 282 bits (721), Expect = 3e-80 Identities = 186/530 (35%), Positives = 276/530 (52%), Gaps = 19/530 (3%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLP--GSGIRHVLTRHEQGAGFMADGYAR 88 T G ALV L +GVDT FG+PGV EL+ GL G IR V +RHEQGA +MA GYA Sbjct: 18 TGGDALVAGLHRWGVDTFFGVPGVQLDELFDGLQRGGGDIRVVHSRHEQGAAYMALGYAM 77 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 V+GKPGVC V+ GPG+ N A+ AYA + +L ++S +SA + + +G LHE DQ Sbjct: 78 VTGKPGVCAVVPGPGLLNAGAALSTAYACNARVLCLTSTVNSALIDRRYGALHEINDQDG 137 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208 + +T +SA A ++P L+ A+ + RPRPV + IP D+LA + A+ Sbjct: 138 LLRSLTKWSARATHASEIPGLLDEAFRQLLTGRPRPVALEIPPDILAQTGFFTYPDAL-- 195 Query: 209 RPGRGVPCSE--ALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGK 266 P P ++ A+ AA +A AR PM++ G GA AG + AL+E + AP+ + G+ Sbjct: 196 -PSLANPLADPAAIEQAATLIAGARNPMIVVGSGAQEAGREVRALAELIQAPIVSRHMGR 254 Query: 267 GLL--PPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDI 324 G++ D L A A+L P W + D+V+ +G+ + W L +++ +D+ Sbjct: 255 GVVRSDDDYALPAAAAL---PHW---PDVDVVIGIGSRLTQLREWGMGGGL--KVVHIDL 306 Query: 325 DPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAPLQA 384 D + N P AV + DA + L+ L ++ AP A A +RA R A Sbjct: 307 DQSEINRIAPPAVGIVADAAEATAKLVDALAEKNLSPAPRTAEFAAIRAAFREEVATEIQ 366 Query: 385 LHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIG 444 LD I AA+ D +MTQ+ Y YA PR++++ + GTLGYG +G Sbjct: 367 PQVGYLDVIRAAMAEDDVFVDEMTQVGYASRYALPVYTPRTYVNSSYQGTLGYGFATALG 426 Query: 445 AKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLG-LDI 503 A++GA +R + + GDGGF+YT ELATA PL+ +++N+ G +R Sbjct: 427 AQVGAGKRRVISVNGDGGFMYTMPELATAVLH-RIPLIAIVFNDGNFGNVRRIQANKYGG 485 Query: 504 EPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 + NPDF L ++G A + + + L L G G LIE+ Sbjct: 486 RLIASNLHNPDFVALAHSFGVAGLKAEGPEGLATALETARGLEGPVLIEV 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: 765 Number of extensions: 40 Number of successful extensions: 5 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: 555 Length adjustment: 36 Effective length of query: 523 Effective length of database: 519 Effective search space: 271437 Effective search space used: 271437 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