Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF1435 PS417_07295 hypothetical protein
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__WCS417:GFF1435 Length = 541 Score = 439 bits (1128), Expect = e-127 Identities = 257/534 (48%), Positives = 331/534 (61%), Gaps = 17/534 (3%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T G+ LV+LL YGVD VFGIPGVHT+ELYRGL S IRHV RHEQGAGFMADGYAR Sbjct: 3 TCGEVLVKLLEGYGVDQVFGIPGVHTVELYRGLARSSIRHVTPRHEQGAGFMADGYARTR 62 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 GKPGVCF+ITGPG+TN+ TA+GQAYADS+P+LVISSV + LG G G LHE +Q AM Sbjct: 63 GKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELPNQSAMM 122 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210 A + AFS +S QLP ++ARA+A+F + RPRPVHI IPLDVL + A + P Sbjct: 123 AGVAAFSHTLMSAAQLPGVLARAFALFQAGRPRPVHIEIPLDVL----VENADALLGSEP 178 Query: 211 ---GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKG 267 R A++ ++ LAAA++P+++AGGGA+ A L L+E L AP+ ++ KG Sbjct: 179 VSVARAGAAPSAVKHMSQLLAAAKKPLILAGGGAIDAAPELTRLAEVLGAPVALTINAKG 238 Query: 268 LLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDI 324 LLP PL G++ + ++AEAD+VLA+GTE+A+TD+ + + G L+RVDI Sbjct: 239 LLPSSHPLLIGSTQTLVATRALVAEADVVLAIGTELAETDYDVTFAGGFEILGALLRVDI 298 Query: 325 DPRKFNDFYPSAVALRGDARQTLEALLVRL---PQEARDSAPAAARVARLRAEIRAAHAP 381 DP + YP VAL DA+ +ALL L P AR+SA A RVA L AE+ Sbjct: 299 DPDQTVRNYPPQVALVADAQIAAQALLTELGSEPLPARNSAWGAQRVAHLWAELTPIWDT 358 Query: 382 LQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLP 440 L+ + LP +A + D TQ Y+GN PR W + TGYGTLGY LP Sbjct: 359 ATRAQTLFLNTVLETLP-NAVLVGDSTQPVYSGNLTLNLDHPRRWFNASTGYGTLGYALP 417 Query: 441 AGIGAKLG-APQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDML 499 A IGA LG +P + L+GDGG +T ELA+A E +P++VLLWNN +I+ M+ Sbjct: 418 AAIGAWLGRGDGQPVVCLIGDGGLQFTLPELASA-VEARTPVIVLLWNNHGYEEIKKYMV 476 Query: 500 GLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 IEPVGV PDF +A GCA Q ++ L LRA + G TLIE+ Sbjct: 477 NRAIEPVGVDIYTPDFIGAAKALGCAAESIQGVESLRVALRAAADRQGPTLIEI 530 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: 796 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: 541 Length adjustment: 36 Effective length of query: 523 Effective length of database: 505 Effective search space: 264115 Effective search space used: 264115 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