Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate AO353_05935 AO353_05935 kynureninase
Query= reanno::pseudo3_N2E3:AO353_05935 (416 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05935 Length = 416 Score = 836 bits (2160), Expect = 0.0 Identities = 416/416 (100%), Positives = 416/416 (100%) Query: 1 MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL 60 MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL Sbjct: 1 MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL 60 Query: 61 IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR 120 IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR Sbjct: 61 IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR 120 Query: 121 VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY 180 VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY Sbjct: 121 VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY 180 Query: 181 MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW 240 MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW Sbjct: 181 MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW 240 Query: 241 VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ 300 VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ Sbjct: 241 VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ 300 Query: 301 TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI 360 TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI Sbjct: 301 TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI 360 Query: 361 AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT 416 AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT Sbjct: 361 AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT 416 Lambda K H 0.322 0.136 0.413 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: 788 Number of extensions: 27 Number of successful extensions: 1 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: 416 Length of database: 416 Length adjustment: 31 Effective length of query: 385 Effective length of database: 385 Effective search space: 148225 Effective search space used: 148225 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate AO353_05935 AO353_05935 (kynureninase)
to HMM TIGR01814 (kynU: kynureninase (EC 3.7.1.3))
# 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/TIGR01814.hmm # target sequence database: /tmp/gapView.30884.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01814 [M=400] Accession: TIGR01814 Description: kynureninase: kynureninase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-108 348.7 0.0 2.6e-108 348.4 0.0 1.1 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 AO353_05935 kynureninase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 AO353_05935 kynureninase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.4 0.0 2.6e-108 2.6e-108 2 400 .] 8 400 .. 7 400 .. 0.91 Alignments for each domain: == domain 1 score: 348.4 bits; conditional E-value: 2.6e-108 TIGR01814 2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmp.kaakealkeeldkWakllveshevg 64 alda+d+l++lR +Falp + viyld NSL++ p +a+++a+ ++++W++ l++s++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 8 LALDAQDPLAHLRHQFALP-----EGVIYLDgNSLGARPvAALERAQAVIAEEWGNGLIRSWN-- 65 78*****************.....99****66***9988356788999999************.. PP TIGR01814 65 kapWleldealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIlleakaFP 123 +a W +l+e+l + la ++a e evvv++++++Nl+k+l +++++ +++R++I++e+++FP lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 66 SAGWRDLPERLGNRLAglIGAGEGEVVVTDTTSINLFKVLGAALRVqamrAPTRRVIVSESSNFP 130 999********999888999************************9888889************** PP TIGR01814 124 sDlyaiesqlklkleveeslvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlfdl 187 +Dly++e + l ++ sl+ v++ e ++ ++ +++ A+v+l++v+Ykt + d+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 131 TDLYIAEGLMDLL-QQGYSLRLVDSPE----------ELAQAIDQDTAVVMLTHVNYKTgYMHDM 184 *******999998.5555565555555..........3334456679************999*** PP TIGR01814 188 aaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelp 251 +a+t++ ++ gal+++DLaH+++ vp++L ++++D+A+ C+YKyln +p + afv+ ++ +l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 185 QAVTALIHECGALAIWDLAHSAGaVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVWVAPQLCDLV 249 **********************99*************************999*******999999 PP TIGR01814 252 rlalwwwhekskrfkmeeklelrp..aafrlsnppvlsvaalka.LelfdqaslealRkkSllLT 313 ++l+ w +s +f+m + e++ a + ++p++s+a++++ Le+f+q+++ lR+kSl+LT lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 250 TQPLSGWFGHSRQFDMASGYEPSSgiARYLCGTQPITSLAMVECgLEIFAQTDMPSLRRKSLALT 314 88765555555666666666666665889999********************************* PP TIGR01814 314 dyleeLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRla 377 d++++Lv++r+a l++itP+++a+r s++s++++ + +av++al++++v+ D+ReP ++R+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 315 DLFIQLVEQRCAA-HDLKLITPREHARRgSHVSFEHP-QGYAVIQALIAQGVIGDYREPRIMRFG 377 ************8.69*********************.*************************** PP TIGR01814 378 PvpLYntfkDvykavevleeile 400 +pLY++f++v++av++l eil+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05935 378 FTPLYTSFTEVFDAVQILGEILD 400 ********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (416 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 10.22 // [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