Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF427 PS417_02175 transcriptional regulator
Query= reanno::pseudo3_N2E3:AO353_12810 (1317 letters) >FitnessBrowser__WCS417:GFF427 Length = 1317 Score = 2471 bits (6404), Expect = 0.0 Identities = 1253/1317 (95%), Positives = 1284/1317 (97%) Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTEL+GL+ + Sbjct: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGLSSKD 60 Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120 AD+ EV DHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLP PMAE Sbjct: 61 ADDAGEVQTDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPTPMAE 120 Query: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD Sbjct: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180 Query: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP Sbjct: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240 Query: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA Sbjct: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300 Query: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ Sbjct: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360 Query: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR Sbjct: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420 Query: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP Sbjct: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480 Query: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVS+GKLNRPCRVYAP Sbjct: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSDGKLNRPCRVYAP 540 Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMATLEGGFGLPH Sbjct: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATLEGGFGLPH 600 Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660 PRIPLPRDLYGS+RANS+GIDLANEHRLASLSCALLATAHNNWKAAPMLGCA+S + P Sbjct: 601 PRIPLPRDLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPMLGCASSEQAAAP 660 Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720 VLNPSDLRDVVGHVQEATV D DNAIQCA++A PIWQATPPAERAAILERAADLME EIQ Sbjct: 661 VLNPSDLRDVVGHVQEATVEDVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQ 720 Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL Sbjct: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPG+GETVGARL Sbjct: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGQGETVGARL 840 Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV Sbjct: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA Sbjct: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020 EAKAGIEKHIQAMRDKGRNVYQVAIAD EE KRGTFVMPTLIEL+SFDELQREIFGPVLH Sbjct: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLH 1020 Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 VVRYKRK+IDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV Sbjct: 1021 VVRYKRKEIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSF RGD L+APDVRLRDAMS+PLTA Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFVRGDALAAPDVRLRDAMSQPLTA 1140 Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200 LKTWAD +K ++LSALC+QFA QSQSGITR L GPTGERNSYAILPREHVLCLA+VE DL Sbjct: 1141 LKTWADGNKFSDLSALCSQFAAQSQSGITRQLAGPTGERNSYAILPREHVLCLADVEGDL 1200 Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260 L+QLAAVLAVGGSAVWPE +L+KAL RLPK++QA+IK VADW KDEVVFDAVLHHG SD Sbjct: 1201 LTQLAAVLAVGGSAVWPETDLTKALFPRLPKEIQAKIKRVADWTKDEVVFDAVLHHGDSD 1260 Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317 QLRAVCQQVA+R GAI+GVQGLSQGET +ALERLVIERALSVNTAAAGGNASLMTIG Sbjct: 1261 QLRAVCQQVAQRGGAIVGVQGLSQGETAVALERLVIERALSVNTAAAGGNASLMTIG 1317 Lambda K H 0.318 0.134 0.386 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: 4529 Number of extensions: 147 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: 1317 Length of database: 1317 Length adjustment: 48 Effective length of query: 1269 Effective length of database: 1269 Effective search space: 1610361 Effective search space used: 1610361 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: 59 (27.3 bits)
Align candidate GFF427 PS417_02175 (transcriptional regulator)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))
# 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/TIGR01238.hmm # target sequence database: /tmp/gapView.25043.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01238 [M=500] Accession: TIGR01238 Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-248 808.8 1.4 1.2e-247 808.2 1.4 1.3 1 lcl|FitnessBrowser__WCS417:GFF427 PS417_02175 transcriptional regu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF427 PS417_02175 transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 808.2 1.4 1.2e-247 1.2e-247 1 499 [. 608 1108 .. 608 1109 .. 0.99 Alignments for each domain: == domain 1 score: 808.2 bits; conditional E-value: 1.2e-247 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74 dlyg+ r ns+G+dlane++l+sl+ ll++a+++++aap++ + a +e+ a pv np d +d+vG+v+ea + lcl|FitnessBrowser__WCS417:GFF427 608 DLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPML-GCASSEQAAAPVLNPSDLRDVVGHVQEATVE 680 89****************************************.77889999*********************** PP TIGR01238 75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakq 148 +v++a+++a++a ++w+at+++eraailer+adl+e ++ l++ll reaGkt+ naiaevreavdflryya q lcl|FitnessBrowser__WCS417:GFF427 681 DVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQPLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQ 754 ************************************************************************** PP TIGR01238 149 vedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviql 222 +++++ ++++++lG+vvcispwnfplaif Gq+aaalaaGn v+akpaeqt+l+aa+av +l+eaG+p gv+ql lcl|FitnessBrowser__WCS417:GFF427 755 ARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQL 828 ************************************************************************** PP TIGR01238 223 lpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvad 293 lpG+Ge+vGa l d+r++Gv+ftGstevarl+++++a r da+ +pliaetGGqnamivds+al+eqvv+d lcl|FitnessBrowser__WCS417:GFF427 829 LPGQGETVGARLVGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQgrpIPLIAETGGQNAMIVDSSALTEQVVID 902 ******************************************99988*************************** PP TIGR01238 294 vlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367 v++safdsaGqrcsalrvlc+qed adrv++++kGam e+++g+p+rl d+Gpvidaeak +++hi++m++k lcl|FitnessBrowser__WCS417:GFF427 903 VVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDK 976 ************************************************************************** PP TIGR01238 368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsr 441 +++v+qv +d e+++gtfv ptl+eld++del++e+fGpvlhvvryk++e+d+++ +ina+GygltlGvh+r lcl|FitnessBrowser__WCS417:GFF427 977 GRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLHVVRYKRKEIDQLIGQINASGYGLTLGVHTR 1050 ************************************************************************** PP TIGR01238 442 ieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 i+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r lcl|FitnessBrowser__WCS417:GFF427 1051 IDETIAKVIDNVNAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 1108 ******************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1317 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: 00:00:00.02 # Mc/sec: 23.80 // [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