Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 7023590 Shewana3_0819 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::ANA3:7023590 (1064 letters) >FitnessBrowser__ANA3:7023590 Length = 1064 Score = 2077 bits (5382), Expect = 0.0 Identities = 1064/1064 (100%), Positives = 1064/1064 (100%) Query: 1 MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR 60 MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR Sbjct: 1 MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR 60 Query: 61 RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED 120 RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED Sbjct: 61 RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED 120 Query: 121 KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR 180 KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR Sbjct: 121 KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR 180 Query: 181 QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA 240 QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA Sbjct: 181 QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA 240 Query: 241 NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI 300 NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI Sbjct: 241 NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI 300 Query: 301 GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG 360 GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG Sbjct: 301 GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG 360 Query: 361 DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ 420 DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ Sbjct: 361 DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ 420 Query: 421 FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP 480 FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP Sbjct: 421 FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP 480 Query: 481 YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK 540 YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK Sbjct: 481 YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK 540 Query: 541 NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA 600 NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA Sbjct: 541 NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA 600 Query: 601 FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ 660 FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ Sbjct: 601 FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ 660 Query: 661 DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI 720 DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI Sbjct: 661 DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI 720 Query: 721 FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA 780 FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA Sbjct: 721 FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA 780 Query: 781 DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS 840 DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS Sbjct: 781 DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS 840 Query: 841 SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN 900 SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN Sbjct: 841 SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN 900 Query: 901 LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS 960 LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS Sbjct: 901 LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS 960 Query: 961 ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG 1020 ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG Sbjct: 961 ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG 1020 Query: 1021 LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1064 LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA Sbjct: 1021 LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1064 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: 3210 Number of extensions: 109 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: 1064 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 1019 Effective search space: 1038361 Effective search space used: 1038361 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 7023590 Shewana3_0819 (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.22860.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-222 725.9 2.5 1.4e-222 725.5 2.5 1.1 1 lcl|FitnessBrowser__ANA3:7023590 Shewana3_0819 bifunctional proli Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023590 Shewana3_0819 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogen # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.5 2.5 1.4e-222 1.4e-222 1 497 [. 533 1039 .. 533 1042 .. 0.98 Alignments for each domain: == domain 1 score: 725.5 bits; conditional E-value: 1.4e-222 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75 d++g+ rkns+G+++++ se++++ + l k ++qa p+v++++ ge + v++p d + vGqv +ad+a lcl|FitnessBrowser__ANA3:7023590 533 DIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQT-LTGEHKTVVSPFDTTQTVGQVAFADKAA 606 89****************************************8776.579999********************** PP TIGR01238 76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150 +++av sa aafa+w+ t+ + ra+ l++ladlle++ el+al+ reaGk++++ i+evreavdf+ryya q++ lcl|FitnessBrowser__ANA3:7023590 607 IEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAK 681 **************************************************************************9 PP TIGR01238 151 dvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqe 212 + +++ + +G++vcispwnfplaif+Gq++aalaaGntv+akpaeqts+i +rav+l ++ lcl|FitnessBrowser__ANA3:7023590 682 KLMSKPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQ 756 999888777799*************************************************************** PP TIGR01238 213 aGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstala 287 aG+p+ v+q lpG G++vG alt+deri+Gv ftGst +a+lin++la+re a +pliaetGGqnam+vdst+ + lcl|FitnessBrowser__ANA3:7023590 757 AGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQP 831 *************************************************************************** PP TIGR01238 288 eqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362 eqvv dv++s+f saGqrcsalrvl++qed+adrv+++++Gamdel++g+p +tdvGpvida ak nl ahi+ lcl|FitnessBrowser__ANA3:7023590 832 EQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHID 906 *************************************************************************** PP TIGR01238 363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlG 437 ++k+++k ++q+ l + +e+g fv+pt++e+d+++ l+ke fGp+lhv+ryka+el++v+d+in++G+gltlG lcl|FitnessBrowser__ANA3:7023590 907 HIKQVGKLIKQMSLPA--GTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLG 979 **************99..8999***************************************************** PP TIGR01238 438 vhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 +hsr+e+ + ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ lcl|FitnessBrowser__ANA3:7023590 980 IHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 1039 *********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1064 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: 20.86 // [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