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) >lcl|FitnessBrowser__Burk376:H281DRAFT_02404 H281DRAFT_02404 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase 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.28500.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 14.81 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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