Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_012706686.1 NGR_RS11860 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::azobra:AZOBR_RS23695 (1235 letters) >NCBI__GCF_000018545.1:WP_012706686.1 Length = 1235 Score = 1656 bits (4288), Expect = 0.0 Identities = 869/1232 (70%), Positives = 974/1232 (79%), Gaps = 9/1232 (0%) Query: 5 TAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAA 64 T AAP APFADFAPPIR T LR AITAAYRRPE ECLP L E A+LP G AA Sbjct: 10 TISTDAAP---APFADFAPPIRTQTTLRQAITAAYRRPETECLPPLVEAATLPRGTRDAA 66 Query: 65 AATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDK 124 A TARKL+ ALRAK +G GVEGL+ EYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDK Sbjct: 67 AGTARKLVEALRAKHKGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDK 126 Query: 125 IAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGV 184 I+ G+W++HLG G S+FVNAATWGL++TGKLTS +++L++ALTRLI+R GEP+IRRGV Sbjct: 127 ISDGNWKSHLGGGRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGV 186 Query: 185 DFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAI 244 D AMRMMGEQFVTG+TI EAL AR +E +GFRYSYDMLGEAA TA DA RYY DY AI Sbjct: 187 DMAMRMMGEQFVTGETIDEALRRARALEQKGFRYSYDMLGEAATTAADAERYYKDYEAAI 246 Query: 245 HAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLN 304 HAIG ASAGRG+YEGPGISIKLSA+HPRY+R QA RVM ELLP+VKALALLAK YDIG N Sbjct: 247 HAIGKASAGRGIYEGPGISIKLSALHPRYARTQAARVMGELLPKVKALALLAKTYDIGFN 306 Query: 305 IDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRL 364 IDAEEADRLELSLDL+E LC D DLA WNG+GFVVQAYGKRCP+V+DF+IDLARR+G R+ Sbjct: 307 IDAEEADRLELSLDLLEELCLDSDLADWNGMGFVVQAYGKRCPFVLDFIIDLARRAGRRI 366 Query: 365 MIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHN 424 M+RLVKGAYWD+EIKRAQLDGL DFPV+TRK++TDVSY+ACARKLL+A +AVFPQFATHN Sbjct: 367 MVRLVKGAYWDAEIKRAQLDGLEDFPVFTRKIHTDVSYIACARKLLSATDAVFPQFATHN 426 Query: 425 AQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVG--PLKRPCRIYAPVGTHETLLA 482 AQTLATI+ MAG DF VGKYEFQCLHGMGEPLY+EVVG L RPCRIYAPVGTHETLLA Sbjct: 427 AQTLATIHHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRENLGRPCRIYAPVGTHETLLA 486 Query: 483 YLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPE 542 YLVRRLLENGANSSFV+RIADP V +D L+ADPV + RA+ GA H IALP L+ Sbjct: 487 YLVRRLLENGANSSFVHRIADPGVSIDALIADPVEIVRAMPVVGAKHEKIALPAELFGAA 546 Query: 543 RANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGS 602 R NSAG+D+S+E LA L+ L ASA + WTAAP LA G +G+ +PV NP D RD VGS Sbjct: 547 RPNSAGLDISNEATLAALTETLKASAAIGWTAAPQLATGAASGETRPVVNPGDHRDRVGS 606 Query: 603 VTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKS 662 VTE SE A A AA +WAA P ERAA L RAAD MQ RMPTLLGLIVREAGKS Sbjct: 607 VTETSEEDAKRAVRLAAEAAPSWAAVSPAERAACLDRAADLMQARMPTLLGLIVREAGKS 666 Query: 663 LPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAA 722 L NAIAEVREAIDFLRYY Q R A HRPLGPV+CISPWNFPLAIF+GQIAAAL A Sbjct: 667 LLNAIAEVREAIDFLRYYAEQTRRTLGQA-HRPLGPVICISPWNFPLAIFTGQIAAALVA 725 Query: 723 GNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGS 782 GNPVLAKPAEETPLIAAE VRILH AG+PA ALQLLPG G VGAALV GVMFTGS Sbjct: 726 GNPVLAKPAEETPLIAAEGVRILHEAGVPASALQLLPGDGRVGAALVAAPQTAGVMFTGS 785 Query: 783 TEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQR 842 TEVARLIQ QLA RL P G PIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQR Sbjct: 786 TEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQR 845 Query: 843 CSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMR 902 CSALR+LCLQED+ADRTLAMLKGA+ EL IG DRL+VDVGPVIS EA+ I HIE MR Sbjct: 846 CSALRVLCLQEDIADRTLAMLKGALHELNIGRTDRLSVDVGPVISAEAKDIIETHIERMR 905 Query: 903 AKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSI 962 GR VE + L AET GTF+ PT+IE+ + +L+REVFGPVLHV+R+ RD+LD L+D I Sbjct: 906 GLGRKVEQIGLAAETEAGTFVPPTIIELEKLADLQREVFGPVLHVIRYRRDNLDRLIDDI 965 Query: 963 NATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAG 1022 NATGYGLTFGLHTR+D TI VT RI AGN+YVNRN IGAVVGVQPFGG GLSGTGPKAG Sbjct: 966 NATGYGLTFGLHTRLDETIAHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAG 1025 Query: 1023 GPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGG 1082 GPLYL RL++ P L + +WL KG TAEA + SA+G Sbjct: 1026 GPLYLGRLVTPAPVP--PQHSSVHIDPTLLDFAKWLDGKGATAEAETARNAGSSSALGLD 1083 Query: 1083 AELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGL 1142 EL GPVGERNLY LH RGRVLL+P T +GL QL A LATGNS VDA L L+ L Sbjct: 1084 LELPGPVGERNLYALHPRGRVLLVPATESGLYHQLAAALATGNSVVVDAACGLQASLKSL 1143 Query: 1143 PPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAG 1202 P ++A RV + DW GP A LVEGD ER+ +N+ +A LPGP++LVQAA+ E +A Sbjct: 1144 PHSVALRVSWSKDWAADGPFAGALVEGDAERIRQVNKAIAALPGPLVLVQAASGEEIAR- 1202 Query: 1203 RGEGYDLDLLLNERSVSVNTAAAGGNASLVAM 1234 + Y L+ L+ E S S+NTAAAGGNASL+ + Sbjct: 1203 NPDAYCLNWLVEEVSTSINTAAAGGNASLMTI 1234 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: 3764 Number of extensions: 168 Number of successful extensions: 5 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: 1235 Length of database: 1235 Length adjustment: 48 Effective length of query: 1187 Effective length of database: 1187 Effective search space: 1408969 Effective search space used: 1408969 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: 59 (27.3 bits)
Align candidate WP_012706686.1 NGR_RS11860 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
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.1596480.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-230 751.8 2.7 1.6e-230 751.7 0.7 1.9 2 NCBI__GCF_000018545.1:WP_012706686.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012706686.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 751.7 0.7 1.6e-230 1.6e-230 1 496 [. 541 1034 .. 541 1038 .. 0.99 2 ? -0.9 0.1 0.023 0.023 180 196 .. 1117 1133 .. 1113 1146 .. 0.82 Alignments for each domain: == domain 1 score: 751.7 bits; conditional E-value: 1.6e-230 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71 +l+g +r ns+G+d++ne +l+ l e l+++aa + aap + a+ge++pv+np d++d vG v+e+ NCBI__GCF_000018545.1:WP_012706686.1 541 ELFGAARPNSAGLDISNEATLAALTETLKASAAIGWTAAPQL-ATGAASGETRPVVNPGDHRDRVGSVTET 610 79****************************************.67789*********************** PP TIGR01238 72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 +++++++av a +a++ w a+ ++eraa+l+r+adl++ +mp+l++l+vreaGk+l naiaevrea+dfl NCBI__GCF_000018545.1:WP_012706686.1 611 SEEDAKRAVRLAAEAAPSWAAVSPAERAACLDRAADLMQARMPTLLGLIVREAGKSLLNAIAEVREAIDFL 681 *********************************************************************** PP TIGR01238 143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213 ryya+q + +l++ +++lG+v+cispwnfplaiftGqiaaal+aGn v+akpae+t+liaa++v +l+ea NCBI__GCF_000018545.1:WP_012706686.1 682 RYYAEQTRRTLGQA-HRPLGPVICISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEGVRILHEA 751 ************99.******************************************************** PP TIGR01238 214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281 Gvpa+++qllpG G vGaal + ++ aGv+ftGstevarli+ +la+r + +pliaetGGqnamiv NCBI__GCF_000018545.1:WP_012706686.1 752 GVPASALQLLPGDGR-VGAALVAAPQTAGVMFTGSTEVARLIQAQLADRLSPAgrpIPLIAETGGQNAMIV 821 **************9.*********************************9986666*************** PP TIGR01238 282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352 ds+alaeqvv dv+asafdsaGqrcsalrvlc+qed+adr+l ++kGa++el++g+ rl dvGpvi ae NCBI__GCF_000018545.1:WP_012706686.1 822 DSSALAEQVVGDVIASAFDSAGQRCSALRVLCLQEDIADRTLAMLKGALHELNIGRTDRLSVDVGPVISAE 892 *********************************************************************** PP TIGR01238 353 akqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkv 423 ak+ +++hie+m++ ++kv q+ l++ e+e gtfv+pt++el++l++l++evfGpvlhv+ry++d+ld++ NCBI__GCF_000018545.1:WP_012706686.1 893 AKDIIETHIERMRGLGRKVEQIGLAA--ETEAGTFVPPTIIELEKLADLQREVFGPVLHVIRYRRDNLDRL 961 *************************9..999**************************************** PP TIGR01238 424 vdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyr 494 +d ina+Gyglt+G+h+r +et++++++r+k+Gn+yvnrn++GavvGvqpfGG+GlsGtGpkaGGplyl r NCBI__GCF_000018545.1:WP_012706686.1 962 IDDINATGYGLTFGLHTRLDETIAHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGR 1032 **********************************************************************9 PP TIGR01238 495 lt 496 l+ NCBI__GCF_000018545.1:WP_012706686.1 1033 LV 1034 97 PP == domain 2 score: -0.9 bits; conditional E-value: 0.023 TIGR01238 180 qiaaalaaGntviakpa 196 q+aaala+Gn+v+ a NCBI__GCF_000018545.1:WP_012706686.1 1117 QLAAALATGNSVVVDAA 1133 89**********98766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1235 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 63.08 // [ok]
This GapMind analysis is from Apr 09 2024. 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