Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate SMc02263 SMc02263 hypothetical protein
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Smeli:SMc02263 Length = 537 Score = 368 bits (945), Expect = e-106 Identities = 232/531 (43%), Positives = 300/531 (56%), Gaps = 18/531 (3%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T G+ LV LL GV+ VFGIPGVHT+ELYRGL S IRHV RHEQGAGFMADGYARVS Sbjct: 7 TVGETLVDLLEANGVEVVFGIPGVHTVELYRGLAASKIRHVTPRHEQGAGFMADGYARVS 66 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 GKPGV VITGPG+TN TA+ QA DS+P+LVIS VN SLG G G LHE DQ M Sbjct: 67 GKPGVALVITGPGLTNTITAMAQARQDSIPMLVISGVNRRDSLGHGRGLLHELPDQNGMM 126 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPV-AHDWSAAVARR 209 + +S L+P LP ++ RA+AV S RP PVHI IP DV+A + A A R Sbjct: 127 KTLALYSHTLLNPADLPLVVDRAFAVLLSGRPGPVHIEIPTDVMALKIEGRPAKPAAATR 186 Query: 210 PGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLL 269 P SE L+ AA A A RP+++ GGGAL A + L+ER+ AP+ T+V +G+L Sbjct: 187 PRSD---SETLQRAAILCAEAARPVILCGGGALTAEAEVRELAERIGAPVVTTVNARGML 243 Query: 270 PPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTD---FWRERLPLSGELIRVDIDP 326 PL AS + ++ EADLVLA+GTEM TD + PL LIR DID Sbjct: 244 -AGHPLRVPASPSLKAVRALLREADLVLALGTEMGQTDYDLYADGGFPLLKNLIRTDIDA 302 Query: 327 RKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAA---HAPLQ 383 + +A+++ A+ +L LP D A A V R A +AA P Sbjct: 303 AQLARGPQAALSILSGAKAATAGILGFLP----DHAAAKDGVLRAEAARKAALKELTPKM 358 Query: 384 ALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLPAG 442 +++ I LP D + D TQ Y GN + R+W + TGYG+LGY PA Sbjct: 359 LAEIGVVETIYRTLP-DCTIVGDSTQAVYAGNLYCDAPRQRAWFNSATGYGSLGYAPPAA 417 Query: 443 IGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLD 502 +GA + RP + LVGDGGF ++ E+ +A + ++ +V L+WNND +I M+ Sbjct: 418 VGAAVADRGRPVICLVGDGGFQFSLAEIGSA-VDANARVVFLVWNNDGYREIESYMVESG 476 Query: 503 IEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 I P GV P PDF L +AYG + + +L R L A + G +LIE+ Sbjct: 477 ITPEGVKPSAPDFLLTAKAYGLPAERLATVKDLPRALAAAASRPGPSLIEI 527 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: 802 Number of extensions: 39 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: 537 Length adjustment: 36 Effective length of query: 523 Effective length of database: 501 Effective search space: 262023 Effective search space used: 262023 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