Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Synpcc7942_0139 Synpcc7942_0139 acetolactate synthase 3 catalytic subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__SynE:Synpcc7942_0139 Length = 612 Score = 221 bits (562), Expect = 8e-62 Identities = 172/544 (31%), Positives = 252/544 (46%), Gaps = 51/544 (9%) Query: 27 QKTLTAGQALVRLLANYGVDTVFGIPGVHTL----ELYRGLPGSGIRHVLTRHEQGAGFM 82 Q+ T AL+ L +GV +FG PG L EL+R ++H+L RHEQGA Sbjct: 9 QQRATGAYALIDSLCQHGVKHIFGYPGGAILPIYDELHRAEAAGRVQHILVRHEQGAVHA 68 Query: 83 ADGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHE 142 AD Y+R +G+ GVCF +GPG TN+ T I A DS+P++V++ ++G E Sbjct: 69 ADAYSRATGEVGVCFATSGPGATNLVTGIATAQMDSIPMVVVTGQVPRTAIGT--DAFQE 126 Query: 143 TQDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLA-----AP 197 T D +T PI S + P + ++A A+ + S RP PV I +P DV P Sbjct: 127 T-DIYGITLPIVKHSYVVRDPRDMARIVAEAFHIAQSGRPGPVLIDVPKDVGTEEFDYVP 185 Query: 198 VAHDWSAAVARRP-GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSER 254 VA RP RG P + A + ARRP+L GGGA+ AG L A +ER Sbjct: 186 VAPGDIRLPGYRPTTRGNP--RQIAQAIALVKVARRPLLYVGGGAITAGAHAELRAFAER 243 Query: 255 LAAPLFTSVAGKGLLPPDAPLNAGASLCVAPGWE--MIAEADLVLAVGTEMADTDFWR-E 311 P+ T++ GKG PL G + ++E DL++AVG D + + Sbjct: 244 FQLPVTTTLMGKGAFDERHPLALGMLGMHGTAYANFAVSECDLLIAVGARFDDRVTGKLD 303 Query: 312 RLPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQ-----EARDSAPAAA 366 ++I VDIDP + V + GD RQ L LL R + +A + P Sbjct: 304 EFASKAQVIHVDIDPAEVGKNRVPEVPIVGDVRQVLNELLARAEEQISADDATRTQPWLD 363 Query: 367 RVARLRAEIRAAHAPLQALH-------QAILDRIAAALPADAFVSTDMTQLAYTGNYAFA 419 R+A + E PLQ + Q ++ + A P DA+ +TD+ Q F Sbjct: 364 RIAYWKREY-----PLQIPYYADVLSPQQVIHSLGEAAP-DAYFTTDVGQHQMWA-AQFI 416 Query: 420 SRAPRSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDS 479 PR W+ G GT+G+G+PA +GA++ P + + GD L QEL T + + + Sbjct: 417 KNGPRRWISSAGLGTMGFGMPAAMGAQMALPDDTVICVAGDASILMNIQELGTLA-QYNI 475 Query: 480 PLVVLLWNNDALGQIR-------DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDL 532 P+ V++ NN G +R D+ G+ PDF L A+G + Sbjct: 476 PIKVVVVNNGWQGMVRQWQEAFYDERYSNSNMERGM----PDFVKLAEAFGIKGMRVSHP 531 Query: 533 DELE 536 DEL+ Sbjct: 532 DELQ 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: 872 Number of extensions: 61 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: 612 Length adjustment: 37 Effective length of query: 522 Effective length of database: 575 Effective search space: 300150 Effective search space used: 300150 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