Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::HerbieS:HSERO_RS00905 (1230 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 1081 bits (2795), Expect = 0.0 Identities = 591/1047 (56%), Positives = 723/1047 (69%), Gaps = 37/1047 (3%) Query: 21 LPTPS-PLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSS 79 LPT + P RA ITAA+ RDE EAV LL Q ++ LA LV +VR + S Sbjct: 33 LPTGAEPARARITAAWLRDETEAVNDLLVQASLPPVEREKVIDLAADLVTRVRARAKDQS 92 Query: 80 GVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFV 139 V++ M ++ LSSEEGV LMC+AEALLRIPD+ TAD+LI DK+ +W+KHLG+S SLFV Sbjct: 93 AVESFMRQYDLSSEEGVLLMCVAEALLRIPDKATADKLIRDKLGDANWKKHLGQSESLFV 152 Query: 140 NAATWGLLITGKLVSTSSE--SGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQT 197 NA+TWGL++TGKLV+ + + T A+ RL+G+ GEP IR V AMR++G+QFV G+T Sbjct: 153 NASTWGLMLTGKLVNLAGDIRHDFTGALRRLVGRAGEPAIRLAVRQAMRIMGHQFVMGRT 212 Query: 198 IEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGP 257 I EALD + E YRYSYDMLGE+ALT A+ Y Q Y +AI AIG D P Sbjct: 213 IGEALDRCAQKEYAVYRYSYDMLGESALTSETAERYQQDYRNAIAAIGARGPFANHTDAP 272 Query: 258 GISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMM 317 ISVKLSALHPRY A+ +L +L +L LA ++ I L++DAEEADRLELSLD++ Sbjct: 273 SISVKLSALHPRYEVAKRELARRDLTAKLLELSQLAMKHGIALSVDAEEADRLELSLDIL 332 Query: 318 EVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKR 377 + A P LAG++GLG VVQ Y KR PFVID+L++ AR +GRR +RLVKGAYWD+E+KR Sbjct: 333 GDVFAHPSLAGWNGLGIVVQAYSKRTPFVIDWLIETARGSGRRWYVRLVKGAYWDAEVKR 392 Query: 378 AQVDGLEGYPVYTRKVHTDLSYLTCAQKLL-AATDVIYPQFATHNAHTLAAIYHWARQHQ 436 AQ +GL GYPVYTRK +TD+SYL CA+KL A ++IYPQFATHNAHT+AA++H A+ Sbjct: 393 AQENGLPGYPVYTRKPNTDVSYLACARKLFDAGIELIYPQFATHNAHTIAAVHHLAKGRP 452 Query: 437 IDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFV 496 YE+Q LHGMG LY +V+G NL CRVYAPVG+H+ LL YLVRRLLENGAN+SFV Sbjct: 453 ---YEYQRLHGMGTDLYAEVIGAQNLNVPCRVYAPVGTHEDLLPYLVRRLLENGANTSFV 509 Query: 497 NQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQL 556 N++VDE++P+ LV DP ETVR+ +PHP I +P LYGE RKNS G++ SN++ L+ L Sbjct: 510 NRVVDESLPVRELVADPCETVRSFASIPHPRIPLPVNLYGELRKNSMGVNFSNDNELKAL 569 Query: 557 GQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRA 616 + ++ W A PL+ A SA A V NPAD R+VVG A A V+ AL Sbjct: 570 AET-VNAKSGPWTATPLV---PGATSAGATVQVTNPADRRQVVGSYVSADSATVEKALAN 625 Query: 617 ATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFL 676 A W PA RAA+LE AA+ LE E +AL VREAGK LP+AIAE+REA DFL Sbjct: 626 AVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCVREAGKGLPDAIAEIREAADFL 685 Query: 677 RYYAIASRH-------------DGNVL---AWGPVVCISPWNFPLAIFIGEVSAALAAGN 720 RYYA +R + N L G VCISPWNFPLAIF+G+V+AALAAGN Sbjct: 686 RYYATMARRYFGQPEQLPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGN 745 Query: 721 VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST 780 V+AKPAEQT+LI H AVQLLHEAG+P LQ LPG G TVGAALT D RV GV FTGST Sbjct: 746 SVIAKPAEQTSLIGHAAVQLLHEAGVPADVLQYLPGDGATVGAALTRDPRVAGVAFTGST 805 Query: 781 EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD 840 E A INR LA R LIAETGGQNA+I DSSAL EQ+V+D +SSAF Sbjct: 806 ETAWAINRALAARNAP---------IAALIAETGGQNAMIADSSALPEQIVKDAVSSAFQ 856 Query: 841 SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH 900 SAGQRCSA R+L +QEDIAD+ AML GAMAEL+VG P +LS D+GPVID +AR+ L+DH Sbjct: 857 SAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTDVGPVIDEDARKILVDH 916 Query: 901 IERMRASARAVHQLPLGEECQ-HGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALP 959 RM A+ + ++ L +GTF AP EI LA L RE+FGPVLHV+R++ L Sbjct: 917 AARMDQEAKKIGEVALDPATTGNGTFFAPRAYEIPGLATLTREIFGPVLHVIRWKGSELD 976 Query: 960 QLIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSG 1019 +++D INATGYGLTLG+HSRID+T+EF+ RA VGN YVNRN +GAVVGVQPFGGEG SG Sbjct: 977 KVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSG 1036 Query: 1020 TGPKAGGPLYLKRLQRNAQLHEELTRA 1046 TGPKAGGP YL R L T A Sbjct: 1037 TGPKAGGPHYLFRFAGERTLTINTTAA 1063 Score = 40.0 bits (92), Expect = 1e-06 Identities = 40/126 (31%), Positives = 54/126 (42%), Gaps = 23/126 (18%) Query: 1090 LPGPTGERNTLGFAPRGLVLCAAG---SVGTLLNQLAAAFATGN---------TALVDER 1137 LPGPTGE N L RG+ +C + + L Q+AAA A GN T+L+ Sbjct: 702 LPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHA 761 Query: 1138 SAAIL-PSGLPAPV-------RAAIRRASQLDAEPLQAALVDSHQAAHW--RARLAAREG 1187 + +L +G+PA V A + A D A S + A W LAAR Sbjct: 762 AVQLLHEAGVPADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETA-WAINRALAARNA 820 Query: 1188 ALVPLI 1193 + LI Sbjct: 821 PIAALI 826 Score = 39.7 bits (91), Expect = 1e-06 Identities = 19/26 (73%), Positives = 21/26 (80%) Query: 1203 LWRLLAERALCINTTAAGGNASLMTI 1228 L+R ER L INTTAAGGNASL+TI Sbjct: 1047 LFRFAGERTLTINTTAAGGNASLLTI 1072 Lambda K H 0.319 0.134 0.389 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: 2993 Number of extensions: 145 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 1230 Length of database: 1074 Length adjustment: 46 Effective length of query: 1184 Effective length of database: 1028 Effective search space: 1217152 Effective search space used: 1217152 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: 58 (26.9 bits)
Align candidate N515DRAFT_4232 N515DRAFT_4232 (L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate 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.1810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-214 696.7 2.0 1.1e-213 696.3 2.0 1.1 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 N515DRAFT_4232 L-proline dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 696.3 2.0 1.1e-213 1.1e-213 1 496 [. 546 1051 .. 546 1055 .. 0.98 Alignments for each domain: == domain 1 score: 696.3 bits; conditional E-value: 1.1e-213 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdi 64 +lyge rkns+Gv+++n++elk l e +++ + a p+v + + + g + v+npadr+++ lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 546 NLYGELRKNSMGVNFSNDNELKALAETVNAK-SGPWTATPLVPGAT-SAGATVQVTNPADRRQV 607 59***********************999765.679*******6655.5566667********** PP TIGR01238 65 vGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktl 128 vG ad a+v++a+ avaa w ++a+ raaile++a+ le + e++al+vreaGk l lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 608 VGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCVREAGKGL 671 **************************************************************** PP TIGR01238 129 snaiaevreavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftG 179 +aiae+rea dflryya ++ +++ + + +G++vcispwnfplaif+G lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 672 PDAIAEIREAADFLRYYATMARRYFGQPEQLPgptgesnqlflngRGVFVCISPWNFPLAIFLG 735 **************************997777999***************************** PP TIGR01238 180 qiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGv 243 q+aaalaaGn+viakpaeqtsli av+ll+eaGvpa v+q lpG G++vGaalt d+r+aGv lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 736 QVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAGVPADVLQYLPGDGATVGAALTRDPRVAGV 799 **************************************************************** PP TIGR01238 244 iftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcs 307 +ftGste+a in+ala r+++ ++liaetGGqnami ds+al+eq+v+d ++saf+saGqrcs lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 800 AFTGSTETAWAINRALAARNAPIAALIAETGGQNAMIADSSALPEQIVKDAVSSAFQSAGQRCS 863 **************************************************************** PP TIGR01238 308 alrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkv 371 a rvl+vqed+ad+v ++ Gam elkvg p +l tdvGpvid++a++ l+ h +m + akk+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 864 AARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKI 927 **************************************************************** PP TIGR01238 372 aqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGyglt 435 +v l+ + +gtf ap ++e+ l+ l +e+fGpvlhv+r+k +eldkvvd+ina+Gyglt lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 928 GEVALDP-ATTGNGTFFAPRAYEIPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLT 990 *****99.78999*************************************************** PP TIGR01238 436 lGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496 lG+hsri++tv +i++ra+vGn+yvnrn++GavvGvqpfGGeGlsGtGpkaGGp+yl+r+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 991 LGIHSRIDDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTGPKAGGPHYLFRFA 1051 ***********************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1074 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: 20.59 // [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