Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3021 Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)
Query= reanno::psRCH2:GFF3021 (1053 letters) >FitnessBrowser__psRCH2:GFF3021 Length = 1053 Score = 2078 bits (5384), Expect = 0.0 Identities = 1053/1053 (100%), Positives = 1053/1053 (100%) Query: 1 MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60 MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL Sbjct: 1 MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60 Query: 61 IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120 IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW Sbjct: 61 IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120 Query: 121 ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180 ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK Sbjct: 121 ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180 Query: 181 LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240 LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA Sbjct: 181 LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240 Query: 241 EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300 EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA Sbjct: 241 EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300 Query: 301 DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360 DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK Sbjct: 301 DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360 Query: 361 GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420 GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV Sbjct: 361 GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420 Query: 421 SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480 SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL Sbjct: 421 SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480 Query: 481 LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540 LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM Sbjct: 481 LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540 Query: 541 NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600 NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA Sbjct: 541 NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600 Query: 601 RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660 RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR Sbjct: 601 RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660 Query: 661 EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720 EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA Sbjct: 661 EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720 Query: 721 LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780 LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC Sbjct: 721 LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780 Query: 781 FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840 FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ Sbjct: 781 FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840 Query: 841 RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900 RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL Sbjct: 841 RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900 Query: 901 KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960 KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI Sbjct: 901 KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960 Query: 961 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG Sbjct: 961 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020 Query: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD Sbjct: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053 Lambda K H 0.319 0.136 0.396 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: 3243 Number of extensions: 94 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: 1053 Length of database: 1053 Length adjustment: 45 Effective length of query: 1008 Effective length of database: 1008 Effective search space: 1016064 Effective search space used: 1016064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 58 (26.9 bits)
Align candidate GFF3021 Psest_3079 (delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain))
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.27564.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-211 688.0 0.2 5e-211 687.4 0.2 1.2 1 lcl|FitnessBrowser__psRCH2:GFF3021 Psest_3079 delta-1-pyrroline-5-c Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3021 Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 687.4 0.2 5e-211 5e-211 2 497 .. 528 1030 .. 527 1033 .. 0.98 Alignments for each domain: == domain 1 score: 687.4 bits; conditional E-value: 5e-211 TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74 l+g+ rkns+G++++++++ +l + + +++++qaap++++++ a g v+ p++ +++vGq ++a+a+ lcl|FitnessBrowser__psRCH2:GFF3021 528 LFGN-RKNSQGINMNIQNQWTELASAYQPFLERQWQAAPVISGRTLA-GTPSEVRCPYELNKVVGQAQFASAD 598 7898.************************************877766.66678******************** PP TIGR01238 75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyak 147 ++++a+d a ++w+at+ + raa+lerl dlle+h el+al+ eaGk+l++ i+evreavdf+ryya+ lcl|FitnessBrowser__psRCH2:GFF3021 599 QARQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVREAVDFCRYYAQ 671 ************************************************************************* PP TIGR01238 148 qvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaarave 208 q++ +l++e k +G++vc+spwnfplai++Gqi+aal+aGntv+akpaeqtsliaara+e lcl|FitnessBrowser__psRCH2:GFF3021 672 QARLKLGREELKGptgernelfhegRGVFVCVSPWNFPLAIYLGQITAALVAGNTVLAKPAEQTSLIAARALE 744 *********99989*********************************************************** PP TIGR01238 209 llqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamiv 281 l+ eaG+p +i +lpG G+++G + d+r+ Gv ftGst++ar in++la++e + ++liaetGGqnamiv lcl|FitnessBrowser__psRCH2:GFF3021 745 LMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVCFTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIV 817 ************************************************************************* PP TIGR01238 282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeak 354 dstal+eqv++d + saf saGqrcsalrvl+vq+d+adrv++l+kGam el+vg ++ + d+Gpvid+ea+ lcl|FitnessBrowser__psRCH2:GFF3021 818 DSTALPEQVIKDAVGSAFTSAGQRCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAR 890 ************************************************************************* PP TIGR01238 355 qnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdki 427 + llahi+++k+ ++ +a+++ + +g fvap++fe+d +++lkke fGpvlhvvry a +l+kvv i lcl|FitnessBrowser__psRCH2:GFF3021 891 EGLLAHIQQLKSEGRLIAEATVPA---GLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960 *********************998...678******************************************* PP TIGR01238 428 nakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 n +GygltlGvhsr+eet +ie+ a+vGn+yvnrn++GavvGvqpfGG lsGtGpkaGGp yl r+ + lcl|FitnessBrowser__psRCH2:GFF3021 961 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAGGPSYLLRFAN 1030 *******************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1053 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 19.22 // [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