Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF1160 PGA1_c11750 bifunctional protein PutA
Query= reanno::Phaeo:GFF1160 (1158 letters) >FitnessBrowser__Phaeo:GFF1160 Length = 1158 Score = 2282 bits (5914), Expect = 0.0 Identities = 1158/1158 (100%), Positives = 1158/1158 (100%) Query: 1 MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60 MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN Sbjct: 1 MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60 Query: 61 AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120 AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP Sbjct: 61 AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120 Query: 121 SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180 SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK Sbjct: 121 SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180 Query: 181 EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240 EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA Sbjct: 181 EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240 Query: 241 ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300 ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE Sbjct: 241 ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300 Query: 301 ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360 ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV Sbjct: 301 ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360 Query: 361 KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420 KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS Sbjct: 361 KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420 Query: 421 AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480 AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE Sbjct: 421 AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480 Query: 481 NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540 NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT Sbjct: 481 NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540 Query: 541 LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600 LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL Sbjct: 541 LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600 Query: 601 SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660 SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY Sbjct: 601 SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660 Query: 661 AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720 AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH Sbjct: 661 AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720 Query: 721 EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780 EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE Sbjct: 721 EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780 Query: 781 TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840 TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA Sbjct: 781 TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840 Query: 841 LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900 LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG Sbjct: 841 LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900 Query: 901 IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960 IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN Sbjct: 901 IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960 Query: 961 LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020 LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML Sbjct: 961 LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020 Query: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA Sbjct: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080 Query: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV Sbjct: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140 Query: 1141 CVDTTAAGGNAALLGGMG 1158 CVDTTAAGGNAALLGGMG Sbjct: 1141 CVDTTAAGGNAALLGGMG 1158 Lambda K H 0.317 0.132 0.387 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: 3626 Number of extensions: 133 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: 1158 Length of database: 1158 Length adjustment: 47 Effective length of query: 1111 Effective length of database: 1111 Effective search space: 1234321 Effective search space used: 1234321 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: 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