Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02404 H281DRAFT_02404 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::Cup4G11:RR42_RS20125 (1333 letters) >FitnessBrowser__Burk376:H281DRAFT_02404 Length = 1312 Score = 1759 bits (4557), Expect = 0.0 Identities = 917/1345 (68%), Positives = 1065/1345 (79%), Gaps = 45/1345 (3%) Query: 1 MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60 MA+TTLGVK+DD R RL+ A ++RTPHWLIKQAIF YLE++E+G +P E S Sbjct: 1 MASTTLGVKVDDLLRSRLRDAATRLERTPHWLIKQAIFAYLEKIEQGQLPPELS------ 54 Query: 61 EGAADGADAFDGAA----SDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLE 116 G A AD DGA+ DGA PFL+FAQ+VQPQSVLRAAITAAYRRPE ECVP LL Sbjct: 55 -GVAGSADMADGASVEPDEDGAAHPFLDFAQNVQPQSVLRAAITAAYRRPEPECVPFLLG 113 Query: 117 QARLPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEAL 176 QARLP A A+A L LR + G G V+GLI EFSLSSQEGVALMCLAEAL Sbjct: 114 QARLPANLAGDVQALAAKLVETLRGKSKGGG----VEGLIHEFSLSSQEGVALMCLAEAL 169 Query: 177 LRIPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKAL 236 LRIPD+ATRDALIRDKIS +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E LS AL Sbjct: 170 LRIPDRATRDALIRDKISKGDWKSHVGQAPSLFVNAATWGLMITGKLVTTNSETNLSSAL 229 Query: 237 TRIIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAM 296 TR+IGKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA Sbjct: 230 TRLIGKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAAT 289 Query: 297 TEADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGR 356 TEADAQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALHPRYSR+Q ER + EL R Sbjct: 290 TEADAQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHPRYSRSQQERTMSELLPR 349 Query: 357 LKSLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPF 416 ++SL +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PELAGWNGIGFVVQ YQKRCPF Sbjct: 350 VRSLAILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELAGWNGIGFVVQAYQKRCPF 409 Query: 417 VIDYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARK 476 VI+Y++DLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+K Sbjct: 410 VIEYIVDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKK 469 Query: 477 LLSVPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536 LL PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V GPL+ GK Sbjct: 470 LLGAPDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTGPLSAGK 529 Query: 537 FNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMH 596 NRPCR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+ +++ +L+ADPV ++ Sbjct: 530 LNRPCRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADENVAIQDLIADPVEEASKI- 588 Query: 597 ADEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLG 656 LG PH +I PR LYG R NS G+DLSNEHRLASLSSALLA + A P+L Sbjct: 589 ---VPLGAPHAKIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLA 645 Query: 657 TEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAA 716 + + VRNP+D RD+VG V EAS V AAL AV AAPIWQATP + RA Sbjct: 646 DDQIV---LGNARDVRNPADHRDLVGTVVEASAEHVSAALAHAVAAAPIWQATPVEARAD 702 Query: 717 ALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRP 776 L RAA+L+EAQM +LMG++VREAGK+ +NA++E+REA+DFLRYY+ Q+R FS+DTHRP Sbjct: 703 CLARAADLLEAQMHTLMGLVVREAGKSLANAVSEIREAIDFLRYYSTQIRSEFSNDTHRP 762 Query: 777 LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAV 836 LGPVVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAV Sbjct: 763 LGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAV 822 Query: 837 QLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQN 896 QLLPG GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD G+P+PLIAETGGQN Sbjct: 823 QLLPGDGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPEGKPIPLIAETGGQN 882 Query: 897 AMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGN 956 AMIVDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM ELT+GN Sbjct: 883 AMIVDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELTVGN 942 Query: 957 PDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIEL 1016 PDRLSTDVGPVID +A+ I HI AMR KGR+V Q + C GTFV PTLIEL Sbjct: 943 PDRLSTDVGPVIDVDAKRGIDAHIAAMREKGRKVEQL----PMPEGCAQGTFVPPTLIEL 998 Query: 1017 DSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEV 1076 DSI+EL+REVFGPVLHVVRY R+ LD LL QI TGYGLT+GIHTRIDETI H++ RA V Sbjct: 999 DSIDELKREVFGPVLHVVRYRRSQLDQLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHV 1058 Query: 1077 GNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDT-V 1135 GN+YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+ P + +A V Sbjct: 1059 GNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLAQALIVDV 1118 Query: 1136 GGADETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASAAGLSVTLPGPTG 1193 A E G + L L++W A+RE P L A C+ + + AG + L GPTG Sbjct: 1119 PQAAEKGD---NPSAALTALRDWLIAERE----PQLAARCDGYLSHMPAGATAVLSGPTG 1171 Query: 1194 ERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRV 1253 ERNTYTL R VLC+A + Q AAVLA G++A++ E L +LP +++S Sbjct: 1172 ERNTYTLGARGTVLCIASTASGARAQFAAVLATGNRALF-EGAAGEQLVTQLPASLKSYA 1230 Query: 1254 RLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-----HGEPNIAIE 1308 + + +T FDAVL GDSD+L + +++A RPGPI+SVQG+A G+ + A+E Sbjct: 1231 SVRKN---AETPFDAVLFEGDSDELLTLVKEVAKRPGPIVSVQGVASRALESGDEDYALE 1287 Query: 1309 RLLIERSLSVNTAAAGGNASLMTIG 1333 RLL ERS+SVNTAAAGGNA+LMTIG Sbjct: 1288 RLLTERSVSVNTAAAGGNANLMTIG 1312 Lambda K H 0.318 0.133 0.383 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: 4000 Number of extensions: 153 Number of successful extensions: 10 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: 1333 Length of database: 1312 Length adjustment: 49 Effective length of query: 1284 Effective length of database: 1263 Effective search space: 1621692 Effective search space used: 1621692 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: 59 (27.3 bits)
Align candidate H281DRAFT_02404 H281DRAFT_02404 (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.8550.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-243 793.8 0.9 4e-243 793.3 0.9 1.2 1 lcl|FitnessBrowser__Burk376:H281DRAFT_02404 H281DRAFT_02404 L-proline dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_02404 H281DRAFT_02404 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 ! 793.3 0.9 4e-243 4e-243 1 499 [. 603 1102 .. 603 1103 .. 0.99 Alignments for each domain: == domain 1 score: 793.3 bits; conditional E-value: 4e-243 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdi 64 +lyg r ns+G+dl+ne++l+sl++ ll++a++ ++aap++++++ g+a+ v+npad++d+ lcl|FitnessBrowser__Burk376:H281DRAFT_02404 603 NLYGAERLNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLADDQIVLGNARDVRNPADHRDL 666 59************************************************************** PP TIGR01238 65 vGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktl 128 vG+v ea+a++v++a+ avaa+++w+at+ + ra +l r+adlle +m +l++l+vreaGk+l lcl|FitnessBrowser__Burk376:H281DRAFT_02404 667 VGTVVEASAEHVSAALAHAVAAAPIWQATPVEARADCLARAADLLEAQMHTLMGLVVREAGKSL 730 **************************************************************** PP TIGR01238 129 snaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntvi 192 na++e+rea+dflryy+ q++ +++++++++lG+vvcispwnfplaif+Gq+aaalaaGntv+ lcl|FitnessBrowser__Burk376:H281DRAFT_02404 731 ANAVSEIREAIDFLRYYSTQIRSEFSNDTHRPLGPVVCISPWNFPLAIFMGQVAAALAAGNTVL 794 **************************************************************** PP TIGR01238 193 akpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlin 256 akpaeqt+liaa+av +l+eaGvpag++qllpG Ge+vGaal +d+r + v+ftGstevarlin lcl|FitnessBrowser__Burk376:H281DRAFT_02404 795 AKPAEQTPLIAAQAVRILREAGVPAGAVQLLPGDGETVGAALVADPRTRAVMFTGSTEVARLIN 858 **************************************************************** PP TIGR01238 257 kalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqed 317 k+l+ r d++ +pliaetGGqnamivds+alaeqvvadv++s+fdsaGqrcsalrvlc+q+d lcl|FitnessBrowser__Burk376:H281DRAFT_02404 859 KTLSGRLDPEgkpIPLIAETGGQNAMIVDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDD 922 *******987777*************************************************** PP TIGR01238 318 vadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddve 381 vadr+l+++ Gam el vg+p rl tdvGpvid +ak+ + ahi +m++k++kv q+ + + lcl|FitnessBrowser__Burk376:H281DRAFT_02404 923 VADRTLEMLTGAMRELTVGNPDRLSTDVGPVIDVDAKRGIDAHIAAMREKGRKVEQLPMPE--G 984 **********************************************************999..9 PP TIGR01238 382 sekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieet 445 + +gtfv+ptl+eld++delk+evfGpvlhvvry++++ld+++++i ++GygltlG+h+ri+et lcl|FitnessBrowser__Burk376:H281DRAFT_02404 985 CAQGTFVPPTLIELDSIDELKREVFGPVLHVVRYRRSQLDQLLEQIRTTGYGLTLGIHTRIDET 1048 **************************************************************** PP TIGR01238 446 vrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 ++++ +ra+vGn+yvnrn++GavvGvqpfGGeGlsGtGpkaGG+lyl+rl+ +r lcl|FitnessBrowser__Burk376:H281DRAFT_02404 1049 IAHVISRAHVGNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATR 1102 **************************************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1312 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 15.46 // [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