Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Pf1N1B4_1489 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
Query= reanno::pseudo3_N2E3:AO353_12810 (1317 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 Length = 1317 Score = 2497 bits (6471), Expect = 0.0 Identities = 1266/1317 (96%), Positives = 1288/1317 (97%) Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATL+EL+GL E Sbjct: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLSELNGLNGKE 60 Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120 D+ E+HVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE Sbjct: 61 VDDAGEIHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 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 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP Sbjct: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540 Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMATLEGGFGLPH Sbjct: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATLEGGFGLPH 600 Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660 PRIPLPRDLYG+ERANSSGID+ANEHRLASLSCALLATAHNNWKAAPMLGCA+S+ETP P Sbjct: 601 PRIPLPRDLYGAERANSSGIDMANEHRLASLSCALLATAHNNWKAAPMLGCASSSETPAP 660 Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720 VLNPSDLRDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILERAADLME EIQ Sbjct: 661 VLNPSDLRDVVGHVQEATVEDVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQ 720 Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL Sbjct: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVR+L+EAGIPEGVLQLLPGRGETVGARL Sbjct: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLLIEAGIPEGVLQLLPGRGETVGARL 840 Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV Sbjct: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA Sbjct: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020 EAKAGIEKHIQAMRDKGRNVYQVAIA+ EE KRGTFVMPTLIELESFDELQREIFGPVLH Sbjct: 961 EAKAGIEKHIQAMRDKGRNVYQVAIANSEEVKRGTFVMPTLIELESFDELQREIFGPVLH 1020 Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV Sbjct: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGD ++APDVRLRDAMSKPLTA Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDAIAAPDVRLRDAMSKPLTA 1140 Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200 LK WADS+K T+LS LC QFA QSQSGITR L GPTGERNSYAILPREHVLCLA+VE DL Sbjct: 1141 LKAWADSNKFTDLSTLCVQFAAQSQSGITRVLAGPTGERNSYAILPREHVLCLADVEGDL 1200 Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260 L+QLAAVLAVGGSAVWP+ E KAL ARLPK++QARIK VADW KDEVV DAVLHHGHSD Sbjct: 1201 LTQLAAVLAVGGSAVWPDAEPGKALFARLPKEIQARIKRVADWTKDEVVIDAVLHHGHSD 1260 Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317 QLRAVCQQVAKRAGAI+GV GLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG Sbjct: 1261 QLRAVCQQVAKRAGAIVGVHGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 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: 4518 Number of extensions: 145 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 Pf1N1B4_1489 (Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
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.23938.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-247 806.1 1.0 7.7e-247 805.6 1.0 1.2 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 Transcriptional repressor of Put Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 805.6 1.0 7.7e-247 7.7e-247 1 499 [. 608 1108 .. 608 1109 .. 0.99 Alignments for each domain: == domain 1 score: 805.6 bits; conditional E-value: 7.7e-247 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrk 62 dlyg r ns G+d+ane++l+sl+ ll++a+++++aap++ + a +++ pv np d + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 608 DLYGAERANSSGIDMANEHRLASLSCALLATAHNNWKAAPML-GCASSSETPAPVLNPSDLR 668 89****************************************.5566667788********* PP TIGR01238 63 divGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvrea 124 d+vG+v+ea ++v++a+++a++a+++w+at+++eraailer+adl+e ++ l++ll rea lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 669 DVVGHVQEATVEDVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQPLMGLLAREA 730 ************************************************************** PP TIGR01238 125 GktlsnaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaala 186 Gkt+ naiaevreavdflryya q+++++ ++++++lG+vvcispwnfplaif Gq+aaala lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 731 GKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAAALA 792 ************************************************************** PP TIGR01238 187 aGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGs 248 aGn v+akpaeqt+l+aa+av ll eaG+p gv+qllpGrGe+vGa l d+r++Gv+ftGs lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 793 AGNPVLAKPAEQTPLVAAQAVRLLIEAGIPEGVLQLLPGRGETVGARLVGDDRVKGVMFTGS 854 ************************************************************** PP TIGR01238 249 tevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcs 307 tevarl+++++a r da+ +pliaetGGqnamivds+al+eqvv+dv++safdsaGqrcs lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 855 TEVARLLQRNVAGRLDAQgrpIPLIAETGGQNAMIVDSSALTEQVVIDVVSSAFDSAGQRCS 916 ****************99988***************************************** PP TIGR01238 308 alrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakak 369 alrvlc+qed adrv++++kGam e+++g+p+rl d+Gpvidaeak +++hi++m++k++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 917 ALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDKGR 978 ************************************************************** PP TIGR01238 370 kvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakG 431 +v+qv +++ e+++gtfv ptl+el+++del++e+fGpvlhvvryk++++d+++ +ina+G lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 979 NVYQVAIANSEEVKRGTFVMPTLIELESFDELQREIFGPVLHVVRYKRKDIDQLIGQINASG 1040 ************************************************************** PP TIGR01238 432 ygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplyly 493 ygltlGvh+ri+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplyly lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 1041 YGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLY 1102 ************************************************************** PP TIGR01238 494 rltrvr 499 rl+++r lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1489 1103 RLLSTR 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: 00:00:00.03 # Mc/sec: 21.65 // [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