Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate PfGW456L13_223 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__pseudo13_GW456_L13:PfGW456L13_223 Length = 1316 Score = 2478 bits (6422), Expect = 0.0 Identities = 1255/1317 (95%), Positives = 1288/1317 (97%), Gaps = 1/1317 (0%) Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATL+EL+G T+ + Sbjct: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLSELNGSTK-D 59 Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120 +D+ + +DHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE Sbjct: 60 SDDSVDAPLDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 119 Query: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD Sbjct: 120 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 179 Query: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLV+THNEAGLTSSLSRIIGKSGEP Sbjct: 180 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVSTHNEAGLTSSLSRIIGKSGEP 239 Query: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFE KGFRYSYDMLGEAALTEHDAQKYLA Sbjct: 240 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFETKGFRYSYDMLGEAALTEHDAQKYLA 299 Query: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ Sbjct: 300 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 359 Query: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR Sbjct: 360 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 419 Query: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP Sbjct: 420 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 479 Query: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP Sbjct: 480 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 539 Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMAT+EGGFGLPH Sbjct: 540 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATVEGGFGLPH 599 Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660 PRIPLPRDLYGSERANSSGID+ANEHRLASLSCALLATAHN+WKAAPMLGCA+S+E P P Sbjct: 600 PRIPLPRDLYGSERANSSGIDMANEHRLASLSCALLATAHNHWKAAPMLGCASSSEAPAP 659 Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720 VLNPSDLRDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILERAADLME+EIQ Sbjct: 660 VLNPSDLRDVVGHVQEATVEDVDNAIQCALNAAPIWQATPPAERAAILERAADLMEAEIQ 719 Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL Sbjct: 720 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 779 Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVR++LEAGIPEGVLQLLPGRGETVGA L Sbjct: 780 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGAGL 839 Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 VGDDRVKGVMFTGSTEVARLLQRN+AGRLD+QGRPIPLIAETGGQNAMIVDSSALTEQVV Sbjct: 840 VGDDRVKGVMFTGSTEVARLLQRNIAGRLDSQGRPIPLIAETGGQNAMIVDSSALTEQVV 899 Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLGNPERLSVDIGPVIDA Sbjct: 900 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGNPERLSVDIGPVIDA 959 Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020 EAKAGIEKHIQAMRDKGR+VYQVAIAD EE KRGTFV+PTLIELESFDELQREIFGPVLH Sbjct: 960 EAKAGIEKHIQAMRDKGRSVYQVAIADAEEVKRGTFVIPTLIELESFDELQREIFGPVLH 1019 Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV Sbjct: 1020 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1079 Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140 QPFGGEGLSGTGPKAGGPLYLYRLLSTRP DAIEQSFARGD +APDVRLRDAMSKPLTA Sbjct: 1080 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIEQSFARGDAAAAPDVRLRDAMSKPLTA 1139 Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200 LK WAD+HK +LS LC QFA QSQSGITR L GPTGERNSYAILPREHVLCLAEVE DL Sbjct: 1140 LKAWADNHKFADLSTLCVQFAAQSQSGITRLLAGPTGERNSYAILPREHVLCLAEVEGDL 1199 Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260 L+QLAAVLAVGGSAVWPE +++KAL ARLPKD+QARIKLV+DWNKDEVVFDAVLHHGHSD Sbjct: 1200 LTQLAAVLAVGGSAVWPEADMTKALFARLPKDIQARIKLVSDWNKDEVVFDAVLHHGHSD 1259 Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317 QLRAVCQQ+AKRAGAI+GVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG Sbjct: 1260 QLRAVCQQIAKRAGAIVGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1316 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: 4485 Number of extensions: 149 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: 1317 Length of database: 1316 Length adjustment: 48 Effective length of query: 1269 Effective length of database: 1268 Effective search space: 1609092 Effective search space used: 1609092 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 PfGW456L13_223 (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.22477.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 7.8e-247 805.6 1.0 1.3 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 Transcriptional repressor of Put Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 Transcriptional repressor of PutA and PutP / Proline dehydroge # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 805.6 1.0 7.8e-247 7.8e-247 1 499 [. 607 1107 .. 607 1108 .. 0.99 Alignments for each domain: == domain 1 score: 805.6 bits; conditional E-value: 7.8e-247 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqp 54 dlyg+ r ns G+d+ane++l+sl+ ll++a+++++aap++g a +++ p lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 607 DLYGSERANSSGIDMANEHRLASLSCALLATAHNHWKAAPMLG-CASSSEAPAP 659 89****************************************5.556666778* PP TIGR01238 55 vknpadrkdivGqvseadaaevqeavdsavaafaewsatdakeraailerladl 108 v np d +d+vG+v+ea ++v++a+++a++a+++w+at+++eraailer+adl lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 660 VLNPSDLRDVVGHVQEATVEDVDNAIQCALNAAPIWQATPPAERAAILERAADL 713 ****************************************************** PP TIGR01238 109 leshmpelvallvreaGktlsnaiaevreavdflryyakqvedvldeesakalG 162 +e ++ l++ll reaGkt+ naiaevreavdflryya q+++++ ++++++lG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 714 MEAEIQPLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLG 767 ****************************************************** PP TIGR01238 163 avvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvp 216 +vvcispwnfplaif Gq+aaalaaGn v+akpaeqt+l+aa+av l++eaG+p lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 768 PVVCISPWNFPLAIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIP 821 ****************************************************** PP TIGR01238 217 agviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...v 267 gv+qllpGrGe+vGa l d+r++Gv+ftGstevarl+++++a r d++ + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 822 EGVLQLLPGRGETVGAGLVGDDRVKGVMFTGSTEVARLLQRNIAGRLDSQgrpI 875 ************************************************99888* PP TIGR01238 268 pliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadr 321 pliaetGGqnamivds+al+eqvv+dv++safdsaGqrcsalrvlc+qed adr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 876 PLIAETGGQNAMIVDSSALTEQVVIDVVSSAFDSAGQRCSALRVLCLQEDSADR 929 ****************************************************** PP TIGR01238 322 vltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvk 375 v++++kGam e ++g+p+rl d+Gpvidaeak +++hi++m++k+++v+qv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 930 VIEMLKGAMAESRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDKGRSVYQVA 983 ****************************************************** PP TIGR01238 376 leddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkina 429 +d e+++gtfv ptl+el+++del++e+fGpvlhvvryk++++d+++ +ina lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 984 IADAEEVKRGTFVIPTLIELESFDELQREIFGPVLHVVRYKRKDIDQLIGQINA 1037 ****************************************************** PP TIGR01238 430 kGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtG 483 +GygltlGvh+ri+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 1038 SGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGVQPFGGEGLSGTG 1091 ****************************************************** PP TIGR01238 484 pkaGGplylyrltrvr 499 pkaGGplylyrl+++r lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223 1092 PKAGGPLYLYRLLSTR 1107 ************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1316 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 17.48 // [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