Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::Marino:GFF2744 (1209 letters) >FitnessBrowser__Dino:3608920 Length = 1221 Score = 1263 bits (3267), Expect = 0.0 Identities = 665/1209 (55%), Positives = 848/1209 (70%), Gaps = 19/1209 (1%) Query: 15 RQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIMEKFLAEY 74 R +R +Y A+E ++ + A +LS ER+ +A A V VR + ++ME FLAEY Sbjct: 16 RAQVRAHYTAEETALLKSLAARIKLSAHEREKAAAAGARYVTRVRNETRPSMMEAFLAEY 75 Query: 75 GLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINTATVALLM 134 GL+T EGV LMCLAEALLRVPD TI +LIEDK+ WG H+G +SS L+N +T AL++ Sbjct: 76 GLSTSEGVGLMCLAEALLRVPDADTIDDLIEDKVAPSNWGAHLGHSSSSLVNASTWALML 135 Query: 135 TSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEY 194 T +L + R LR L+KR GEPV+RT GQ+MK +GRQFVLG+ I+E A+E Sbjct: 136 TGKVLDEDPRGPA-RALRGLVKRLGEPVVRTAVGQSMKVLGRQFVLGQTIEEGLKNAREL 194 Query: 195 MAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLAR 254 KG+TYSYDMLGEAARTD DA+RY+ +Y+ AI +IA+ + GDVR +PGISVKLSAL R Sbjct: 195 EKKGFTYSYDMLGEAARTDADARRYHAAYAQAITAIARQATGDVRSSPGISVKLSALHPR 254 Query: 255 YEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELVADPELAGW 314 YEY ++ VM +L+PRA LVK+AA A +GFN+DAEEQDRLDLSLDVIE +++DP+L GW Sbjct: 255 YEYTHRHSVMADLVPRAAALVKQAAQAGIGFNVDAEEQDRLDLSLDVIEAMMSDPDLDGW 314 Query: 315 DGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNGFPVF 374 DGFGVVVQAYG+R+ V++ LY +AE+YDRK MVRLVKGAYWD EIK AQ +G+ FPVF Sbjct: 315 DGFGVVVQAYGRRAGPVIETLYDMAERYDRKIMVRLVKGAYWDTEIKLAQELGVERFPVF 374 Query: 375 TRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYEFQRLHGMG 434 TRK +DVS+++CA LL+ +RIYPQFATHNAH+ +A+L+MA D +EFQRLHGMG Sbjct: 375 TRKNNTDVSYMACAQMLLDRRDRIYPQFATHNAHTCAAVLQMAGNAR-DCFEFQRLHGMG 433 Query: 435 ESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKRITPEEIAK 494 SLH V + G CRIYAPVG H+DLLAYLVRRLLENGANSSFVNQIVD I E I+ Sbjct: 434 ASLHQIVKETEGTRCRIYAPVGAHQDLLAYLVRRLLENGANSSFVNQIVDPDIPAEAISA 493 Query: 495 DPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKG 554 DP+ +E++G+ I + AI P LF RRNS+G+ + +P ++ + R A+ + W Sbjct: 494 DPVSEMEKLGDQIPNPAIRQPSDLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHA 553 Query: 555 GPLIAGEVAGT-EIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWSAKSAEER 613 P++AG T + V +PAD LVG V +AS DV A+ +A F WSA+ ER Sbjct: 554 RPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAEDVACALDAAETGFRDWSARPVSER 613 Query: 614 AACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIRYK--DSG 671 A +RK+ D+YE+N AEL A+TTREAGK++LD +AE+REAVDF ++YANEA R + D G Sbjct: 614 ADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAERLEEEDPG 673 Query: 672 DARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKD 731 RG+ CISPWNFPLAIFTGQI A L GN V+AKPAEQT ++A RAV++M G+P Sbjct: 674 RPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDA 733 Query: 732 AIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNA 791 A+QL+PG G VG LTSD R++GVCFTGST A I+K + +N P+A LVAETGGLNA Sbjct: 734 ALQLLPGDGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNA 793 Query: 792 MIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAMEELGIGDP 851 MIVDSTAL EQ VRD+L SSFQSAGQRCSALR+LYVQ D+ D L+EML GA++ L IGD Sbjct: 794 MIVDSTALHEQAVRDILISSFQSAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDS 853 Query: 852 WLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSVSGIEELEE 911 W L DV PVID +A+ I+ + ++ + G L+K + P+ G +V+PA++ V GI ++E Sbjct: 854 WNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLAAPDSGTYVTPAIVKVGGIADMER 913 Query: 912 EIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971 EIFGPVLHVATF+A ID+VVD INA+ YGLTFG+H+R+D RVE+I RI+VGN YVNRN Sbjct: 914 EIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIVERIQVGNVYVNRN 973 Query: 972 QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK-GETVEREADSNARKVDAKQLQKLIG 1030 QIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF K G++ A A + L + Sbjct: 974 QIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKVGKSTSHPAPQGA-VLGKAALNTALS 1032 Query: 1031 QLDKLK-ASRPE----ARMDAIRPIFGNVPEPL------DAHVEALPGPTGETNRLSNHA 1079 LD A+RP+ RM A+ G V L D + LPGPTGE+NRLS Sbjct: 1033 SLDARNWAARPDRVHILRM-ALSGSTGVVRRALSETAAFDMSPQTLPGPTGESNRLSMVP 1091 Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139 RG VLCLGP E A+ QA AL G VV+ PG+ + + AG P+V G ++ Sbjct: 1092 RGTVLCLGPTPEIAMAQAVQALGAGCAVVIALPGSTPLSQPLSDAGAPVVTLDGTVDCVT 1151 Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199 L + G E V + G + R AL++RDG ++PLI + +R+V+ERHLC+DTTAAG Sbjct: 1152 LTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVDEIAPERYVLERHLCIDTTAAG 1211 Query: 1200 GNASLIAAS 1208 GNA L+AAS Sbjct: 1212 GNAKLLAAS 1220 Lambda K H 0.316 0.133 0.378 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: 3465 Number of extensions: 168 Number of successful extensions: 6 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: 1209 Length of database: 1221 Length adjustment: 47 Effective length of query: 1162 Effective length of database: 1174 Effective search space: 1364188 Effective search space used: 1364188 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: 59 (27.3 bits)
Align candidate 3608920 Dshi_2311 (delta-1-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.25863.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-194 633.4 3.2 7.9e-194 630.7 0.1 2.1 2 lcl|FitnessBrowser__Dino:3608920 Dshi_2311 delta-1-pyrroline-5-ca Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 630.7 0.1 7.9e-194 7.9e-194 1 498 [. 516 1008 .. 516 1010 .. 0.99 2 ! 2.9 0.6 0.0017 0.0017 158 272 .. 1089 1190 .. 1075 1198 .. 0.82 Alignments for each domain: == domain 1 score: 630.7 bits; conditional E-value: 7.9e-194 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75 dl++ r+ns G ++ + +l + ++ a+ +++a p++++ g ++ v +pad+ +vG+v+ea+a++ lcl|FitnessBrowser__Dino:3608920 516 DLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHARPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAED 590 799*9**************************************99999*************************** PP TIGR01238 76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150 v a+d+a + f wsa + era +l++lad+ e ++ el a++ reaGkt+ + iaevreavdflr+ya+++e lcl|FitnessBrowser__Dino:3608920 591 VACALDAAETGFRDWSARPVSERADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAE 665 **************************************************************************8 PP TIGR01238 151 dvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpG 225 +e+ +++G +vcispwnfplaiftGqiaaal+ Gn+v+akpaeqt++iaarav+++++ G+p +++qllpG lcl|FitnessBrowser__Dino:3608920 666 RLEEEDPGRPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDAALQLLPG 740 88888999******************************************************************* PP TIGR01238 226 rGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafd 300 G vG ltsd+riaGv ftGsteva i+kalak ++++l+aetGG namivdstal eq v+d+l s+f+ lcl|FitnessBrowser__Dino:3608920 741 DGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNAMIVDSTALHEQAVRDILISSFQ 815 *************************************************************************** PP TIGR01238 301 saGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvk 375 saGqrcsalr+l+vqedv d++++++ Ga+d l++g +l dv pvida+a+ ++l +i++ ++ + ++ + lcl|FitnessBrowser__Dino:3608920 816 SAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDSWNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLA 890 ****************************************************************99999998887 PP TIGR01238 376 leddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqie 450 d gt+v+p ++++ ++++++e+fGpvlhv +ka+e+d+vvd ina+ yglt+G+h+ri++ v qi lcl|FitnessBrowser__Dino:3608920 891 APD-----SGTYVTPAIVKVGGIADMEREIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIV 960 777.....8****************************************************************** PP TIGR01238 451 krakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 +r++vGnvyvnrn++Ga+vG qpfGGeGlsGtGpkaGGplyl r+ +v lcl|FitnessBrowser__Dino:3608920 961 ERIQVGNVYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKV 1008 ********************************************9886 PP == domain 2 score: 2.9 bits; conditional E-value: 0.0017 TIGR01238 158 akalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGa 232 + ++G+v+c+ p i + q + al aG +v+ t+l + l +aG p ++ G + lcl|FitnessBrowser__Dino:3608920 1089 MVPRGTVLCLGPTP---EIAMAQAVQALGAGCAVVIALPGSTPLS-----QPLSDAGAPVVTL---DGTVD--CV 1150 55688888888853...5778899999999998765555678985.....45889**998775...57777..56 PP TIGR01238 233 altsderiaGviftGstevarlinkalakredapvpliae 272 +lt+ + i+ v+ +G+++ +r ++ al++r+ + +pli + lcl|FitnessBrowser__Dino:3608920 1151 TLTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVD 1190 8*******************************99999975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1221 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 16.48 // [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