Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Pf6N2E2_5475 Acetolactate synthase, large subunit (EC 2.2.1.6)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5475 Length = 545 Score = 446 bits (1146), Expect = e-129 Identities = 263/539 (48%), Positives = 333/539 (61%), Gaps = 17/539 (3%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T G+ LV+LL YGV+ VFGIPGVHT+ELYRGL S IRHV RHEQGAGFMADGYARVS Sbjct: 3 TCGEVLVKLLHAYGVEQVFGIPGVHTVELYRGLARSNIRHVTPRHEQGAGFMADGYARVS 62 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 GKPGVCF+ITGPG+TN+ TA+GQAYADS+P+LVISSV LG G G LHE +Q A+ Sbjct: 63 GKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRNQLGGGRGKLHELPNQAALV 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+A+RP+++AGGGA+ A L L+ERL AP+ ++ KGLLP Sbjct: 182 NRAGAAPSAVAQMAAKLASAQRPLILAGGGAIDAAAELTELAERLGAPVALTINAKGLLP 241 Query: 271 PDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDIDPR 327 PL G++ + ++AEAD+VLA+GTE+A+TD+ + + G L+R+DIDP Sbjct: 242 SRHPLLIGSTQSLVATRALVAEADVVLAIGTELAETDYDITFAGGFEIPGALLRIDIDPD 301 Query: 328 KFNDFYPSAVALRGDARQTLEALLVRLPQ----EARDSAPAAARVARLRAEIRAAHAPLQ 383 + YP +AL DAR A+L L Q E RD R ARLRAE++ + Sbjct: 302 QTVRNYPPYLALVADARVATRAVLDALSQHPLAERRDDW-GTTRAARLRAELQGSWDAAT 360 Query: 384 ALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLPAG 442 LD + ALP FV D TQ YTGN F PR W + TGYGTLGY LPA Sbjct: 361 RAQTLFLDTVLQALPEAVFVG-DSTQPVYTGNLTFNPEQPRRWFNSSTGYGTLGYALPAA 419 Query: 443 IGAKLGAPQ----RPGLV-LVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDD 497 IGA LG RP +V L+GDGG +T ELA+A E +P++VLLWNN +I+ Sbjct: 420 IGAWLGGKDRGHGRPAVVCLIGDGGLQFTLPELASA-VEARTPVIVLLWNNQGYEEIKKY 478 Query: 498 MLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELRHA 556 M+ IEPVGV PDF + RA GCA + + +L L A + G TLIE+ A Sbjct: 479 MVNRAIEPVGVDIYTPDFIGVARALGCAAQAIDGVAQLHAALLAACDRQGPTLIEIDQA 537 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: 821 Number of extensions: 33 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: 545 Length adjustment: 36 Effective length of query: 523 Effective length of database: 509 Effective search space: 266207 Effective search space used: 266207 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