Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate AO356_17755 AO356_17755 hypothetical protein
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17755 Length = 543 Score = 444 bits (1142), Expect = e-129 Identities = 260/535 (48%), Positives = 329/535 (61%), Gaps = 15/535 (2%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T G+ LV+LL YGV+ VFGIPGVHT+ELYRGL S IRHV RHEQGAGFMADGYARVS Sbjct: 3 TCGEVLVKLLEGYGVEQVFGIPGVHTVELYRGLARSSIRHVTPRHEQGAGFMADGYARVS 62 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 GKPGVCF+ITGPG+TN+ TA+GQAYADS+P+LVISSV + LG G G LHE +Q A+ Sbjct: 63 GKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELLNQSALV 122 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210 + AFS +S +LP ++ARA+AVF + RPRPVHI IPLDVL A A+V Sbjct: 123 GGVAAFSHTLMSAAELPGVLARAFAVFQAGRPRPVHIEIPLDVLVED-ADALLASVPVNI 181 Query: 211 GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLLP 270 R A++ A+ LA ARRP+++ GGGA+ A L L+ERL AP+ ++ KGLLP Sbjct: 182 SRAGAAPGAVKQMADLLATARRPLILVGGGAIDARAELTELAERLGAPVALTINAKGLLP 241 Query: 271 PDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDIDPR 327 PL G++ + ++AEAD+VLA+GTE+A+TD+ + + G L+R+DIDP Sbjct: 242 ARHPLLIGSTQSLVVTRALVAEADVVLAIGTELAETDYDITFAGGFEIPGALLRIDIDPD 301 Query: 328 KFNDFYPSAVALRGDARQTLEALLVRL---PQEARDSAPAAARVARLRAEIRAAHAPLQA 384 + YP +AL DA ALL L P R + AR ARLRAE++ + Sbjct: 302 QTVRNYPPHLALVADAGVAARALLDELDQRPLAERQADWGPARAARLRAELQGSWDAATR 361 Query: 385 LHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLPAGI 443 LD + LP FV D TQ YTGN F PR W + TGYGTLGY LPA I Sbjct: 362 AQTVFLDTVLQTLPEAVFVG-DSTQPVYTGNLTFNPEQPRRWFNSSTGYGTLGYALPAAI 420 Query: 444 GAKLGAPQ----RPGLV-LVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDM 498 GA LG RP +V L+GDGG +T ELA+A E +P++VLLWNN +I+ M Sbjct: 421 GAWLGGKDLGHGRPAVVCLIGDGGLQFTLPELASA-VEASTPVIVLLWNNQGYEEIKKYM 479 Query: 499 LGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 L IEPVGV PDF + +A GC + D+ L L A + G TLIE+ Sbjct: 480 LNRAIEPVGVDIYTPDFIGVAKALGCFAQAIDDVPSLRAALLAARERQGPTLIEI 534 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: 842 Number of extensions: 31 Number of successful extensions: 7 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: 543 Length adjustment: 36 Effective length of query: 523 Effective length of database: 507 Effective search space: 265161 Effective search space used: 265161 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