Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate PP_4947 PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_12810 (1317 letters) >FitnessBrowser__Putida:PP_4947 Length = 1317 Score = 2313 bits (5995), Expect = 0.0 Identities = 1165/1317 (88%), Positives = 1235/1317 (93%) Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60 MATTTLGVKLDDPTRERLKAAA SIDRTPHWLIKQAIFNYLEKLEGGATLTEL+G + Sbjct: 1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGHASNP 60 Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120 AD+ EV DH+HQCFLEFAESILPQSVLR++ITAAYRRPE EVVPML+EQARL AP+A+ Sbjct: 61 ADDAGEVQADHSHQCFLEFAESILPQSVLRSAITAAYRRPEQEVVPMLLEQARLSAPLAD 120 Query: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180 ATNKLAASIAEKLRNQKS GGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD Sbjct: 121 ATNKLAASIAEKLRNQKSVGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180 Query: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLV+THNE GLTSSL+RIIGKSGEP Sbjct: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVSTHNETGLTSSLTRIIGKSGEP 240 Query: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300 MIRKGVDMAMRLMGEQFVTGETIAEALANAS+FEAKGFRYSYDMLGEAALTEHDAQKYLA Sbjct: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASRFEAKGFRYSYDMLGEAALTEHDAQKYLA 300 Query: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVM+ELYPRLLSLTLLAKQ Sbjct: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPRLLSLTLLAKQ 360 Query: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420 YDIGLNIDAEEADRLELSLDLLERLCFEP L GWNGIGFVIQAYQKRCPYVIDYVIDLA+ Sbjct: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPSLAGWNGIGFVIQAYQKRCPYVIDYVIDLAK 420 Query: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSY+ACARKLL+VPE IYP Sbjct: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYVACARKLLAVPEAIYP 480 Query: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGK+++GKLNRPCRVYAP Sbjct: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKIADGKLNRPCRVYAP 540 Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600 VGTHETLLAYLVRRLLENGANTSFVNRIAD SISIQELVADPV+SIE+M T EG GLPH Sbjct: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADHSISIQELVADPVASIERMGTQEGSIGLPH 600 Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660 PRIPLPRDLYG+ERANS+GID+ANEHRLASLSCA+LATAHN+WKAAP+L CAAS P Sbjct: 601 PRIPLPRDLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLLACAASESAAAP 660 Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720 VLNP+D RDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILER ADLME+EIQ Sbjct: 661 VLNPADHRDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQ 720 Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780 PLMGLL REAGKTFANAIAEVREAVDFLRYYAVQARNDF+NDAHRPLGPVVCISPWNFPL Sbjct: 721 PLMGLLIREAGKTFANAIAEVREAVDFLRYYAVQARNDFSNDAHRPLGPVVCISPWNFPL 780 Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840 AIF+GQVAAALAAGNPVLAKPAEQTPL+AAQAVR+LLEAGIPEGVLQLLPGRGETVGA L Sbjct: 781 AIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGVLQLLPGRGETVGAGL 840 Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 VGD+RVKGVMFTGSTEVARLLQRNVAGRLD QGRPIPLIAETGGQNAMIVDSSALTEQVV Sbjct: 841 VGDERVKGVMFTGSTEVARLLQRNVAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV 900 Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLG P+RL+VDIGPVIDA Sbjct: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDA 960 Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020 EAKAGIEKHIQ MR+KGR VYQVAIAD E KRGTFVMPTLIEL+SFDEL+REIFGPVLH Sbjct: 961 EAKAGIEKHIQGMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLH 1020 Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080 VVRY R+++DQLI QIN SGYGLTLGVHTRIDETIAKV++ NAGN+YVNRNIVGAVVGV Sbjct: 1021 VVRYNRRNLDQLIEQINNSGYGLTLGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGV 1080 Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140 QPFGGEGLSGTGPKAGGPLYLYRLLSTRP DAI + F + D PD L + + KPL Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIGRHFQQQDGEGTPDRTLHEQLVKPLHG 1140 Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200 LK WA++++L +L+ALC+QFA+QSQSGI R L GPTGERNSY ILPREHVLCLA+ E+DL Sbjct: 1141 LKAWAENNQLADLAALCSQFASQSQSGIARLLPGPTGERNSYTILPREHVLCLADNETDL 1200 Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260 L+Q AAVLAVG SAVW +GE KAL ARLP+++QA++KLVADWNKDEV FDAV+HHG SD Sbjct: 1201 LAQFAAVLAVGSSAVWVDGEPGKALRARLPRELQAKVKLVADWNKDEVAFDAVIHHGDSD 1260 Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317 QLR VCQQVAKRAGAI+GV GLS G+ IALERLVIERA+SVNTAAAGGNASLMTIG Sbjct: 1261 QLRGVCQQVAKRAGAIVGVHGLSSGDHQIALERLVIERAVSVNTAAAGGNASLMTIG 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: 4440 Number of extensions: 155 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 PP_4947 PP_4947 (proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase)
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.2152.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-250 815.3 1.6 1.2e-249 814.9 1.6 1.2 1 lcl|FitnessBrowser__Putida:PP_4947 PP_4947 proline dehydrogenase/1- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4947 PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 814.9 1.6 1.2e-249 1.2e-249 1 499 [. 608 1108 .. 608 1109 .. 0.99 Alignments for each domain: == domain 1 score: 814.9 bits; conditional E-value: 1.2e-249 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73 dlyg r ns+G+d+ane++l+sl+ +l++a+++++aap++ a +e a pv npad++d+vG+v+ea lcl|FitnessBrowser__Putida:PP_4947 608 DLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLL-ACAASESAAAPVLNPADHRDVVGHVQEATV 679 89****************************************.677889999********************* PP TIGR01238 74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146 a+v++a+++a++a+++w+at+++eraailer adl+e ++ l++ll+reaGkt+ naiaevreavdflryya lcl|FitnessBrowser__Putida:PP_4947 680 ADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQPLMGLLIREAGKTFANAIAEVREAVDFLRYYA 752 ************************************************************************* PP TIGR01238 147 kqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagv 219 q++++++++++++lG+vvcispwnfplaiftGq+aaalaaGn v+akpaeqt+liaa+av ll+eaG+p gv lcl|FitnessBrowser__Putida:PP_4947 753 VQARNDFSNDAHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGV 825 ************************************************************************* PP TIGR01238 220 iqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeq 289 +qllpGrGe+vGa l der++Gv+ftGstevarl+++++a r d++ +pliaetGGqnamivds+al+eq lcl|FitnessBrowser__Putida:PP_4947 826 LQLLPGRGETVGAGLVGDERVKGVMFTGSTEVARLLQRNVAGRLDNQgrpIPLIAETGGQNAMIVDSSALTEQ 898 **********************************************9999*********************** PP TIGR01238 290 vvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362 vv+dv++safdsaGqrcsalrvlc+qed adrv++++kGam e ++g p rl d+Gpvidaeak +++hi+ lcl|FitnessBrowser__Putida:PP_4947 899 VVIDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDAEAKAGIEKHIQ 971 ************************************************************************* PP TIGR01238 363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGyglt 435 m++k++ v+qv +d e+++gtfv ptl+eld++delk+e+fGpvlhvvry++++ld+++++in++Gyglt lcl|FitnessBrowser__Putida:PP_4947 972 GMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLHVVRYNRRNLDQLIEQINNSGYGLT 1044 ************************************************************************* PP TIGR01238 436 lGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 lGvh+ri+et++++ + a++Gn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r lcl|FitnessBrowser__Putida:PP_4947 1045 LGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 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: 23.58 // [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