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)
Align candidate GFF1160 PGA1_c11750 (bifunctional protein PutA)
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.12520.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-194 633.6 0.0 1.2e-193 630.1 0.0 2.2 2 lcl|FitnessBrowser__Phaeo:GFF1160 PGA1_c11750 bifunctional protein Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1160 PGA1_c11750 bifunctional protein PutA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 630.1 0.0 1.2e-193 1.2e-193 1 496 [. 521 999 .. 521 1002 .. 0.96 2 ! 0.7 0.0 0.0079 0.0079 238 270 .. 1093 1125 .. 1082 1146 .. 0.88 Alignments for each domain: == domain 1 score: 630.1 bits; conditional E-value: 1.2e-193 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgeka.kaegeaqpvknpadrkdivGqvseadaae 75 dl+ r ns G dl +l+ +++ + +++ a p++++ + a +pv+npad vG+v++a +ae lcl|FitnessBrowser__Phaeo:GFF1160 521 DLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLAKAPeTATTTDEPVRNPADLT-TVGRVQTAGQAE 595 789999************************************96664788899********85.79******9999 PP TIGR01238 76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqved 151 ++ a+++ ++ w+a a+ ra +l+r+adl e + el all reaGktl +++ae+reavdflryya ++ lcl|FitnessBrowser__Phaeo:GFF1160 596 IETALSA----ATPWNAS-AETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARI-- 664 8777665....568*995.899**************************************************99.. PP TIGR01238 152 vldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrG 227 + ++G++ cispwnfplaif Gqiaaala Gn+v+akpaeqt+lia ra++ll+eaGvp +++qllpG+G lcl|FitnessBrowser__Phaeo:GFF1160 665 ----SAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAG 736 ....44579******************************************************************* PP TIGR01238 228 edvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaG 303 + vG altsd+r++Gv+ftGst++a +i+ a+a+ + +pliaetGG namivdstal+eq v+ +++saf+saG lcl|FitnessBrowser__Phaeo:GFF1160 737 A-VGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSIIESAFQSAG 811 *.************************************************************************** PP TIGR01238 304 qrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkledd 379 qrcsalr l++qed+ad+vl+++kGamd l++g p +l td Gpvid+ a+ +lahi++ +a ++ +++++ lcl|FitnessBrowser__Phaeo:GFF1160 812 QRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAP-- 885 ******************************************************************99998765.. PP TIGR01238 380 vesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakv 455 + gtfvaptl+e+ +++l++e+fGpvlhvvr+k+++ld+++ ina+Gyglt+G+h+ri++ v++i +r+++ lcl|FitnessBrowser__Phaeo:GFF1160 886 ---QGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHA 958 ...59*********************************************************************** PP TIGR01238 456 GnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496 Gn+yvnrn++Ga+vG qpfGGeGlsGtGpkaGGp+y+ r+ lcl|FitnessBrowser__Phaeo:GFF1160 959 GNLYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFC 999 **************************************996 PP == domain 2 score: 0.7 bits; conditional E-value: 0.0079 TIGR01238 238 eriaGviftGstevarlinkalakredapvpli 270 e +Gvi+ G +ar i+ la+r+ + pli lcl|FitnessBrowser__Phaeo:GFF1160 1093 EGTSGVIWWGDETTAREIESWLARRNGPILPLI 1125 5578**********************9999998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1158 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: 21.04 // [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