Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_067912680.1 AQZ52_RS14875 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::azobra:AZOBR_RS23695 (1235 letters) >NCBI__GCF_001519075.1:WP_067912680.1 Length = 1205 Score = 1409 bits (3648), Expect = 0.0 Identities = 771/1226 (62%), Positives = 899/1226 (73%), Gaps = 38/1226 (3%) Query: 21 FAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITALRAKPR 80 FAP I P T LR AIT A R PEP+ + L A+LP AATAR LI ALRAK R Sbjct: 7 FAPRISPETPLRRAITQATRIPEPDAVRPLLAAATLPEADRARIAATARALIEALRAKAR 66 Query: 81 GRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLGKGGSM 140 V+ L+ E++LSS EG+ALMCLAEALLRIPD ATRDALIRDK++ G+W AHLG+G + Sbjct: 67 PGRVQALVQEFALSSHEGVALMCLAEALLRIPDDATRDALIRDKLSTGNWAAHLGQGKPL 126 Query: 141 FVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQFVTGQT 200 FVNAATWGL+ITGKLT++ L ALTR++ R GEP+IRRGVD A+RMMGEQFV G+T Sbjct: 127 FVNAATWGLVITGKLTASVDATGLGHALTRMVHRLGEPVIRRGVDVALRMMGEQFVMGET 186 Query: 201 IQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGT----ASAGRGV 256 I++AL AR EA+GF +SYDMLGEAA TA+DAARY Y AIHAIG ASAGRGV Sbjct: 187 IEDALARARRREAQGFAFSYDMLGEAAATAQDAARYLEAYTAAIHAIGQSANRASAGRGV 246 Query: 257 YEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLELS 316 + GPGISIKLSA+HPRY+RAQA RVM EL PRV ALA LAK YDI NIDAEE DRLELS Sbjct: 247 FAGPGISIKLSALHPRYTRAQAHRVMAELAPRVLALAELAKSYDIDFNIDAEETDRLELS 306 Query: 317 LDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWDS 376 LD++E L P LAGW G+GFV+QAY KRCP VID+++DLAR SG R+M+RLVKGAYWD+ Sbjct: 307 LDILERLAHAPVLAGWQGLGFVIQAYQKRCPAVIDWIVDLARSSGRRIMVRLVKGAYWDA 366 Query: 377 EIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMAG 436 EIKRAQ GL DFPVYTRKV+TD++YVACARKLLAA +AVFPQFATHNAQTLA++ +AG Sbjct: 367 EIKRAQEAGLSDFPVYTRKVHTDLAYVACARKLLAARDAVFPQFATHNAQTLASVLHLAG 426 Query: 437 SDFQVGKYEFQCLHGMGEPLYKEVVGP--LKRPCRIYAPVGTHETLLAYLVRRLLENGAN 494 DF G YEFQCLHGMGEPLY+EVVGP L RPCR+YAPVGTHETLLAYLVRRLLENGAN Sbjct: 427 PDFTPGDYEFQCLHGMGEPLYEEVVGPEGLDRPCRVYAPVGTHETLLAYLVRRLLENGAN 486 Query: 495 SSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSDE 554 SSFVNRIADP VPV+ L+ DP AV A GAPH IALP+ L+A +RAN+ G+DL+DE Sbjct: 487 SSFVNRIADPDVPVEALIEDPAAVIAAEPEPGAPHDAIALPQALFA-DRANAQGLDLADE 545 Query: 555 TELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAEA 614 LA L+ ALS SA A G+ A A+PVRNPAD RD+VG V A+ A A Sbjct: 546 PTLAALAEALSGSAAQDHRA------GDPARPAEPVRNPADHRDIVGHVHAATIEDAARA 599 Query: 615 FGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREAI 674 A AAAS W+ATP E RAA+L RAAD M+ L+ L++REAGKS NA+AEVREA+ Sbjct: 600 A--ADAAASRWSATPAEARAAALERAADAMEAARVPLIALLIREAGKSAANALAEVREAV 657 Query: 675 DFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEET 734 DFLRYY Q R + A +PLGPV CISPWNFPLAIF+GQIAAALAAGNPVLAKPA ET Sbjct: 658 DFLRYYAVQARHLPETA--QPLGPVACISPWNFPLAIFTGQIAAALAAGNPVLAKPAPET 715 Query: 735 PLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQLA 794 PL+AAEAVR+LHA GIPA AL LLPG G++GAALV V+GV+FTGST AR IQ+ LA Sbjct: 716 PLVAAEAVRLLHATGIPAAALHLLPGGGKIGAALVAAPEVQGVVFTGSTMTARAIQQSLA 775 Query: 795 GRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQED 854 GRL GA IPLIAETGG NAM+VDSSAL EQVV DV+ASAFDSAGQRCSALR+LCLQ+D Sbjct: 776 GRLNAHGATIPLIAETGGLNAMVVDSSALPEQVVADVLASAFDSAGQRCSALRLLCLQDD 835 Query: 855 VADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLP 914 +ADRTL+MLK AM EL GNP +LA DVGPVISE ARA IAAH+ MRA G V +PL Sbjct: 836 IADRTLSMLKAAMAELAGGNPAQLATDVGPVISERARAGIAAHVARMRAAGFPVTEMPLG 895 Query: 915 AETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLH 974 +TA GTF+APT+IE+ +L EVFGPVLHVVRF + +D+L++ INA+GYGLTFGLH Sbjct: 896 EQTAHGTFVAPTLIELNTPTDLTAEVFGPVLHVVRFRAEAIDSLIEGINASGYGLTFGLH 955 Query: 975 TRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSRR 1034 TRID T+ERV GRI AGN+YVNRN IGAVVGVQPFGG GLSGTGPKAGGPLYL+R Sbjct: 956 TRIDQTVERVCGRIEAGNLYVNRNMIGAVVGVQPFGGRGLSGTGPKAGGPLYLARFAPGA 1015 Query: 1035 PKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNGPVGERNL 1094 + P A A+ +W +G A A S +G A L GPVGERN Sbjct: 1016 VPVLPQGDYPAVPDPALAAFAQWASQQGLAAAAQTAWNAAKASPLGFTATLPGPVGERNT 1075 Query: 1095 YELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVRTTA 1154 Y L RGR+ L Q+ AVLATGN+A + AP +A G PPALAARV Sbjct: 1076 YRLAPRGRIACAATGVEALWQQVAAVLATGNTAVIVAPSPVAARPAGFPPALAARV---- 1131 Query: 1155 DWRD-----VGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDL 1209 +W D V LAA+L++G +R+ +R++A I+ + T L Sbjct: 1132 EWSDEHLTRVPDLAAMLIDGPADRIAEASRQLAAREHAIVPLHTGT------------PL 1179 Query: 1210 DLLLNERSVSVNTAAAGGNASLVAMS 1235 LLL E ++SVNT AAGGNASL+A++ Sbjct: 1180 HLLLEEVTLSVNTTAAGGNASLMALA 1205 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: 3939 Number of extensions: 182 Number of successful extensions: 12 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: 1205 Length adjustment: 47 Effective length of query: 1188 Effective length of database: 1158 Effective search space: 1375704 Effective search space used: 1375704 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_067912680.1 AQZ52_RS14875 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase 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.2726782.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-200 652.3 5.6 2.2e-200 652.3 5.6 1.5 2 NCBI__GCF_001519075.1:WP_067912680.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001519075.1:WP_067912680.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 652.3 5.6 2.2e-200 2.2e-200 2 495 .. 530 1011 .. 529 1014 .. 0.97 2 ? -3.7 0.1 0.17 0.17 180 195 .. 1097 1113 .. 1093 1168 .. 0.73 Alignments for each domain: == domain 1 score: 652.3 bits; conditional E-value: 2.2e-200 TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72 l+++ r n++G+dla e +l+ l e l +aa++++a a+pv+npad++divG+v+ a NCBI__GCF_001519075.1:WP_067912680.1 530 LFAD-RANAQGLDLADEPTLAALAEALSGSAAQDHRAGDPA-------RPAEPVRNPADHRDIVGHVHAAT 592 7888.******************************997544.......679*****************999 PP TIGR01238 73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 +++ +a +a aa++ wsat+a+ raa ler+ad +e l+all+reaGk+ na+aevreavdflr NCBI__GCF_001519075.1:WP_067912680.1 593 IEDAARA--AADAAASRWSATPAEARAAALERAADAMEAARVPLIALLIREAGKSAANALAEVREAVDFLR 661 8876655..6778899******************************************************* PP TIGR01238 144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 yya q+++ l+e a++lG+v cispwnfplaiftGqiaaalaaGn v+akpa +t+l+aa+av ll+ +G NCBI__GCF_001519075.1:WP_067912680.1 662 YYAVQARH-LPET-AQPLGPVACISPWNFPLAIFTGQIAAALAAGNPVLAKPAPETPLVAAEAVRLLHATG 730 ******65.7776.9******************************************************** PP TIGR01238 215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 +pa+++ llpG G+ +Gaal + + ++Gv+ftGst +ar i+++la r +a+ +pliaetGG nam+vd NCBI__GCF_001519075.1:WP_067912680.1 731 IPAAALHLLPGGGK-IGAALVAAPEVQGVVFTGSTMTARAIQQSLAGRLNAHgatIPLIAETGGLNAMVVD 800 ***********999.**********************************9988889*************** PP TIGR01238 283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 s+al+eqvvadvlasafdsaGqrcsalr+lc+q+d+adr+l+++k am el g+p +l tdvGpvi ++a NCBI__GCF_001519075.1:WP_067912680.1 801 SSALPEQVVADVLASAFDSAGQRCSALRLLCLQDDIADRTLSMLKAAMAELAGGNPAQLATDVGPVISERA 871 *********************************************************************** PP TIGR01238 354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 + + ah+ +m+a + v+++ l + ++ +gtfvaptl+el+ +l evfGpvlhvvr++a+ +d+++ NCBI__GCF_001519075.1:WP_067912680.1 872 RAGIAAHVARMRAAGFPVTEMPLGE--QTAHGTFVAPTLIELNTPTDLTAEVFGPVLHVVRFRAEAIDSLI 940 ***********************99..899***************************************** PP TIGR01238 425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 + ina+Gyglt+G+h+ri++tv ++ +r+++Gn+yvnrn++GavvGvqpfGG+GlsGtGpkaGGplyl r+ NCBI__GCF_001519075.1:WP_067912680.1 941 EGINASGYGLTFGLHTRIDQTVERVCGRIEAGNLYVNRNMIGAVVGVQPFGGRGLSGTGPKAGGPLYLARF 1011 *********************************************************************98 PP == domain 2 score: -3.7 bits; conditional E-value: 0.17 TIGR01238 180 qiaaalaaGnt.viakp 195 q+aa la+Gnt vi p NCBI__GCF_001519075.1:WP_067912680.1 1097 QVAAVLATGNTaVIVAP 1113 67777777776334333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1205 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 34.71 // [ok]
This GapMind analysis is from Sep 24 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