Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::ANA3:7023590 (1064 letters) >FitnessBrowser__PV4:5208103 Length = 1059 Score = 1848 bits (4786), Expect = 0.0 Identities = 923/1058 (87%), Positives = 996/1058 (94%) Query: 6 MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65 MFKASEVL GRYDSA LDELF A+T+NYIVDEEQYLSELIKLVPSSD+ I+R+T+RAH+L Sbjct: 1 MFKASEVLTGRYDSATLDELFTAITNNYIVDEEQYLSELIKLVPSSDDEIQRITKRAHDL 60 Query: 66 VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125 V+KVRQ+DKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALI+DKLSGA Sbjct: 61 VHKVRQYDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIDDKLSGA 120 Query: 126 KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185 KWDEHLSKSDS LVNASTWGLMLTGKI+ LDK IDG PS+LL+RLVNRLGEPVIRQAM+A Sbjct: 121 KWDEHLSKSDSTLVNASTWGLMLTGKIISLDKSIDGKPSSLLNRLVNRLGEPVIRQAMLA 180 Query: 186 AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245 AMKIMGKQFVLGRT++EALKNS DKRKLGYTHSYDMLGEAALT KDA+KY+ DY+NAI Sbjct: 181 AMKIMGKQFVLGRTVQEALKNSTDKRKLGYTHSYDMLGEAALTMKDAQKYYQDYSNAIAA 240 Query: 246 LGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 305 LGAQ Y+E+E+PRPTISIKLSALHPRYEVANEDR +TELYDT+I+L+ AR LN+G+SID Sbjct: 241 LGAQQYDESEAPRPTISIKLSALHPRYEVANEDRTMTELYDTLIKLVSQARSLNVGVSID 300 Query: 306 AEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 365 AEEVDRLELSLKLFQKL+N+DA KGWGLLG+VVQAYSKRALPVL W+TRLAK+QGDEIPV Sbjct: 301 AEEVDRLELSLKLFQKLYNSDAAKGWGLLGLVVQAYSKRALPVLCWITRLAKDQGDEIPV 360 Query: 366 RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 425 RLVKGAYWDSELKWAQ AGE YPL+TRKAGTDVSYLACARYLLSDATRGAIYPQFASHN Sbjct: 361 RLVKGAYWDSELKWAQVAGEGGYPLFTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 420 Query: 426 AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 485 AQTVAAI+DMAGDR +EFQRLHGMG+ELYDT+L+E+G VRIYAP+GAHKDLLPYLVRR Sbjct: 421 AQTVAAITDMAGDRLYEFQRLHGMGEELYDTLLAESGVSTVRIYAPVGAHKDLLPYLVRR 480 Query: 486 LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGL 545 LLENGANTSFVHKLVDPKTPIESLVVHPL TL YKTLANNKIV P DIFG++RKNSKG+ Sbjct: 481 LLENGANTSFVHKLVDPKTPIESLVVHPLTTLQSYKTLANNKIVQPIDIFGAERKNSKGI 540 Query: 546 NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKA 605 NMNIISE+EPFFAALDKFK QW AGP+VNG+TL+GE V SP+DTTQ VG+VAFA+ Sbjct: 541 NMNIISESEPFFAALDKFKDQQWSAGPIVNGETLSGETIEVKSPYDTTQIVGKVAFANNQ 600 Query: 606 AIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE 665 AIEQA+ASA AF +W TPVEVRA+ALQKLADLLEENREELIALCTREAGKSIQDGIDE Sbjct: 601 AIEQALASAHNAFGSWCSTPVEVRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660 Query: 666 VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 725 VREAVDFCRYYAVQAKK+M KPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV Sbjct: 661 VREAVDFCRYYAVQAKKMMGKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720 Query: 726 SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG 785 +AALAAGNTVVAKPAEQTSI+GYRAVQLAH+AGIP + LQ+LPGTGATVG +TADERIG Sbjct: 721 TAALAAGNTVVAKPAEQTSIVGYRAVQLAHEAGIPKEALQFLPGTGATVGATITADERIG 780 Query: 786 GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 845 GVCFTGST TAK IN TLA R+GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS Sbjct: 781 GVCFTGSTVTAKRINLTLAQRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 840 Query: 846 AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHI 905 AGQRCSALRVL+LQEDIADRVIDV++GAMDEL IGNP SVKTDVGPVIDATAKANL+AHI Sbjct: 841 AGQRCSALRVLYLQEDIADRVIDVMKGAMDELTIGNPGSVKTDVGPVIDATAKANLNAHI 900 Query: 906 DHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV 965 DHIKQVG+LI Q+ LPAGTENGHFV+PTAVEIDSIKVLEKEHFGPILHVIRYKA++L V Sbjct: 901 DHIKQVGRLINQLELPAGTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKAADLPKV 960 Query: 966 IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1025 ID+INSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG Sbjct: 961 IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020 Query: 1026 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSD 1063 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDS+ Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSE 1058 Lambda K H 0.317 0.133 0.377 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: 3020 Number of extensions: 101 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: 1064 Length of database: 1059 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 1014 Effective search space: 1033266 Effective search space used: 1033266 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 (21.6 bits) S2: 58 (26.9 bits)
Align candidate 5208103 Shew_0615 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.16999.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-219 714.9 1.9 3.1e-219 714.5 1.9 1.1 1 lcl|FitnessBrowser__PV4:5208103 Shew_0615 bifunctional proline d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 714.5 1.9 3.1e-219 3.1e-219 1 497 [. 528 1034 .. 528 1037 .. 0.98 Alignments for each domain: == domain 1 score: 714.5 bits; conditional E-value: 3.1e-219 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaaev 76 d++g rkns+G+++++ se +++ + l k ++++ a piv++++ +ge+ vk+p+d +ivG+v +a+++ + lcl|FitnessBrowser__PV4:5208103 528 DIFGAERKNSKGINMNIISESEPFFAALDKFKDQQWSAGPIVNGET-LSGETIEVKSPYDTTQIVGKVAFANNQAI 602 89****************************************8765.5688888********************** PP TIGR01238 77 qeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqvedv 152 ++a+ sa +af w +t+ + ra l++ladlle++ el+al+ reaGk++++ i+evreavdf+ryya q+++ lcl|FitnessBrowser__PV4:5208103 603 EQALASAHNAFGSWCSTPVEVRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKM 678 **************************************************************************** PP TIGR01238 153 ldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGv 215 +++ + +G++vcispwnfplaif+Gq++aalaaGntv+akpaeqts++ +rav+l +eaG+ lcl|FitnessBrowser__PV4:5208103 679 MGKPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVTAALAAGNTVVAKPAEQTSIVGYRAVQLAHEAGI 754 *999888899****************************************************************** PP TIGR01238 216 pagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvv 291 p ++q+lpG G++vGa++t+deri+Gv ftGst +a++in +la+r+ a +pliaetGGqnam+vdst+ +eqvv lcl|FitnessBrowser__PV4:5208103 755 PKEALQFLPGTGATVGATITADERIGGVCFTGSTVTAKRINLTLAQRDGAIIPLIAETGGQNAMVVDSTSQPEQVV 830 **************************************************************************** PP TIGR01238 292 advlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367 dv++s+f saGqrcsalrvl++qed+adrv++++kGamdel +g+p+ +tdvGpvida ak nl ahi+++k++ lcl|FitnessBrowser__PV4:5208103 831 NDVVSSSFTSAGQRCSALRVLYLQEDIADRVIDVMKGAMDELTIGNPGSVKTDVGPVIDATAKANLNAHIDHIKQV 906 **************************************************************************** PP TIGR01238 368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrie 443 ++ ++q+ l + +e+g fvapt++e+d+++ l+ke fGp+lhv+ryka +l kv+d in++G+gltlG+hsr+e lcl|FitnessBrowser__PV4:5208103 907 GRLINQLELPA--GTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKAADLPKVIDDINSTGFGLTLGIHSRNE 980 *********99..8999*********************************************************** PP TIGR01238 444 etvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 + + ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ lcl|FitnessBrowser__PV4:5208103 981 GHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 1034 ***************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1059 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: 16.60 // [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