Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate RR42_RS32050 RR42_RS32050 AraC family transcriptional regulator
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS32050 Length = 397 Score = 277 bits (709), Expect = 3e-79 Identities = 154/376 (40%), Positives = 210/376 (55%), Gaps = 6/376 (1%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 G A APV++ SLG++ +MW PQ+ AL + R++ D RGHG S P GP SV +L D Sbjct: 17 GPASAPVLIFSNSLGTDHTMWAPQVEALGQQFRILRYDTRGHGRSALPPGPSSVAELGSD 76 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134 V+AL+D+L + A F GLSMGG WLG +AP+R + L TA + G +AW R Sbjct: 77 VIALMDALQIQKAAFCGLSMGGLTGMWLGVNAPQRFTRIVLANTAPRIGTHEAWNTRIEG 136 Query: 135 SRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTAD 194 DG L + + RWF+ + R+++ GYAA C A+ D D Sbjct: 137 VLRDGMTPLVEGSLQRWFTPAFVSAAGNQLDDLRQVLTGLDARGYAANCAAVRDADLREA 196 Query: 195 LSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLRE 254 + I P LVIAG DPST + LAD I AR+ L AAH++N EQ T L + Sbjct: 197 VKTIPVPVLVIAGSADPSTTAEQGRALADAIPGARYLELE-AAHLSNREQPARFTEALLD 255 Query: 255 HIVG-AGYARGRRA----AHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWG 309 + G A A GR A + G+ VRR++LG AHVDRS+A T FQ+ ITR AWG Sbjct: 256 FLGGDAQQAAGRPANDGERYQAGLAVRRAVLGSAHVDRSLAKLNPLTEEFQNLITRYAWG 315 Query: 310 DIWSRPGLDHELRRLLTIAVLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGV 369 +IW+R GL R L+TIA++ A+ EL +H+RAA V D + EVLL T++Y GV Sbjct: 316 EIWTREGLPRHSRSLITIAMMVALNRGEELKLHLRAAANNKVSRDEVKEVLLQTAIYCGV 375 Query: 370 PNSNLGFALGKQALAD 385 P +N F + ++ A+ Sbjct: 376 PAANSAFHMAEEVFAE 391 Lambda K H 0.318 0.132 0.392 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: 411 Number of extensions: 16 Number of successful extensions: 2 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: 400 Length of database: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate RR42_RS32050 RR42_RS32050 (AraC family transcriptional regulator)
to HMM TIGR02425 (pcaC: 4-carboxymuconolactone decarboxylase (EC 4.1.1.44))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02425.hmm # target sequence database: /tmp/gapView.3380.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02425 [M=123] Accession: TIGR02425 Description: decarb_PcaC: 4-carboxymuconolactone decarboxylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-58 181.7 0.2 5e-58 180.8 0.2 1.4 1 lcl|FitnessBrowser__Cup4G11:RR42_RS32050 RR42_RS32050 AraC family transcr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS32050 RR42_RS32050 AraC family transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.8 0.2 5e-58 5e-58 3 122 .. 273 392 .. 271 393 .. 0.98 Alignments for each domain: == domain 1 score: 180.8 bits; conditional E-value: 5e-58 TIGR02425 3 eryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgr 71 ery++Gl+vrravlG ahvdr+la+ + +++efq+lit++aWG++W+r+gl+++ rsl+tia+++al+r lcl|FitnessBrowser__Cup4G11:RR42_RS32050 273 ERYQAGLAVRRAVLGSAHVDRSLAKLNPLTEEFQNLITRYAWGEIWTREGLPRHSRSLITIAMMVALNR 341 89******************************************************************* PP TIGR02425 72 eeelalhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 eel+lh+raaan+ v++d++kevllq+aiy+GvPaan+a+++a+ev+ae lcl|FitnessBrowser__Cup4G11:RR42_RS32050 342 GEELKLHLRAAANNKVSRDEVKEVLLQTAIYCGVPAANSAFHMAEEVFAEE 392 ************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (397 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.80 // [ok]
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