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)
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