Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate CCNA_00846 CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::SB2B:6938573 (1058 letters) >FitnessBrowser__Caulo:CCNA_00846 Length = 1029 Score = 956 bits (2470), Expect = 0.0 Identities = 529/1027 (51%), Positives = 673/1027 (65%), Gaps = 14/1027 (1%) Query: 31 DEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVGIDAFLQQYSLETQEG 90 DE A + +L+A P S E+ A + + A LV R+ +K +V ++FLQ++SL T+EG Sbjct: 14 DEAAVIADLLAAKPLSSEDRAAVRAEAEALVRGARRSVRKQGVV--ESFLQEFSLGTREG 71 Query: 91 IILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGKIVQL 150 + LMCLAEALLR PD +T D LIA+K+ A W H+ SDS+ VNASTWGLMLTGKIV+ Sbjct: 72 LALMCLAEALLRTPDDDTRDKLIAEKIGSADWASHLGGSDSLFVNASTWGLMLTGKIVEP 131 Query: 151 DKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKRKLGY 210 D+ + +L RLGEPVIR A+ A++IMG+QFVLGRTIE +K AA + G Sbjct: 132 DETARNDMPGFIKKLAGRLGEPVIRAAVGQAIRIMGEQFVLGRTIEAAIKRAAAE---GD 188 Query: 211 THSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPRYEVA 270 S+DMLGE A T DA +Y + YA+AI+ +G +S+KLSAL PRYE Sbjct: 189 MCSFDMLGEGARTAADAARYEKAYADAIETVGKLSNGAGPEAGHGVSVKLSALCPRYEAT 248 Query: 271 NEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGWGLLG 330 +EDRV ELY ++L + A N+ IDAEE DRL LSLKL KL + W LG Sbjct: 249 HEDRVWEELYPRTLRLAKIAARHNLNFTIDAEEADRLALSLKLLDKLCREPELGDWTGLG 308 Query: 331 IVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLFTRKA 390 + VQAY KR V+ L L++E G + +RLVKGAYWDSE+K AQ AG YP+FT K Sbjct: 309 LAVQAYQKRCGEVIARLKALSEETGRRLMVRLVKGAYWDSEIKRAQVAGRPDYPVFTTKP 368 Query: 391 ATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDR--KFEFQRLHGMGQEL 448 ATD+SYL A+ L+ A +Y QFA+HNA T+AA+ M + K E QRLHGMG+ L Sbjct: 369 ATDLSYLVNAKALIEAAPH--LYAQFATHNAHTLAAVVRMAKNTGVKIEHQRLHGMGEAL 426 Query: 449 YDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVTHP 508 Y T+R YAP+G H+DLLPYLVRRLLENGANTSFVH L+D + P+E +VT P Sbjct: 427 YKAADDLYDGITLRAYAPVGGHEDLLPYLVRRLLENGANTSFVHALLDERVPVEKVVTDP 486 Query: 509 LKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPL 568 + T++ + + KI P +++G R NS GL++++ ++ E AA+ SAGPL Sbjct: 487 IDTVEAHPD-RHAKIPTPINVYGERRVNSAGLDLSVKADRERLSAAVAAQDGVTLSAGPL 545 Query: 569 VNGETLSGEVR-DVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANA 627 V G+ ++G +++P N VG V+ A A I++A A A +W R RA Sbjct: 546 VGGKVVAGGAPLPLIAPANDQKTVGVVSEAQSAQIDEAFKLARAAQPAWDRAGGVARAQV 605 Query: 628 LQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPG 687 L+ + D LE N E LIAL +REAGK++ DGI EVREAVDFCRYYA+ A+ + E+L G Sbjct: 606 LRAMGDALEANIERLIALLSREAGKTLSDGIAEVREAVDFCRYYAMLAEDQFGEAEILKG 665 Query: 688 PTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQ 747 P GE N L L GRGVFVCISPWNFPLAIF GQ+AAALA GN V+AKPAEQT LI F AV+ Sbjct: 666 PVGETNSLRLAGRGVFVCISPWNFPLAIFTGQIAAALAAGNAVLAKPAEQTPLIAFEAVK 725 Query: 748 LAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIP 807 L H AG+ +L LPG G VGA LTS E + GV FTG T TA IN+ LA R G I+P Sbjct: 726 LYHAAGLDPRLLALLPGRGETVGAALTSHEDLDGVAFTGGTDTAWRINQTLAARQGPIVP 785 Query: 808 LIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKG 867 IAETGG N M VD+T+Q EQV++DV+ SAF SAGQRCSALR+L+L D A+ +++ LKG Sbjct: 786 FIAETGGLNGMFVDTTAQREQVIDDVIVSAFGSAGQRCSALRLLFLPHDTADHIIEGLKG 845 Query: 868 AMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAP 927 AMD L LG+P TDVGPVIDA AK L+ H+ +K +++H L+ P G G F AP Sbjct: 846 AMDALVLGDPALAVTDVGPVIDAEAKDALDKHLVRLKSDAKVLHALAAPAG---GTFFAP 902 Query: 928 TAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALEVA 987 EI + L +E FGP+LHVVRYK L+KV + + +GLTLGIHSR E A +V Sbjct: 903 VLAEIPTADFLEREVFGPVLHVVRYKPENLEKVAGALAARRYGLTLGIHSRIESFAADVQ 962 Query: 988 DKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGG 1047 V GN Y+NR+ GAVVGVQPFGG+GLSGTGPKAGGPH L RF E+ + NITA GG Sbjct: 963 RLVPAGNAYVNRSMTGAVVGVQPFGGEGLSGTGPKAGGPHALLRFAVERALSVNITAQGG 1022 Query: 1048 NATLLSL 1054 + LL+L Sbjct: 1023 DPALLNL 1029 Lambda K H 0.317 0.134 0.380 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: 2548 Number of extensions: 99 Number of successful extensions: 9 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: 1058 Length of database: 1029 Length adjustment: 45 Effective length of query: 1013 Effective length of database: 984 Effective search space: 996792 Effective search space used: 996792 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: 58 (26.9 bits)
Align candidate CCNA_00846 CCNA_00846 (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.25132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-186 606.8 1.5 1.9e-186 606.4 1.5 1.2 1 lcl|FitnessBrowser__Caulo:CCNA_00846 CCNA_00846 proline dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00846 CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 606.4 1.5 1.9e-186 1.9e-186 1 496 [. 505 1008 .. 505 1012 .. 0.99 Alignments for each domain: == domain 1 score: 606.4 bits; conditional E-value: 1.9e-186 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71 ++yge r ns+G+dl+++ ++l++ + ++ + a p+vg+k +a g p+ +pa+ ++ vG vsea lcl|FitnessBrowser__Caulo:CCNA_00846 505 NVYGERRVNSAGLDLSVKADRERLSAAVAAQDGVTLSAGPLVGGKVVAGGAPLPLIAPANDQKTVGVVSEA 575 58********************************************************************* PP TIGR01238 72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 + a+++ea + a aa + w ra +l+++ d le ++ l+all reaGktls+ iaevreavdf+ lcl|FitnessBrowser__Caulo:CCNA_00846 576 QSAQIDEAFKLARAAQPAWDRAGGVARAQVLRAMGDALEANIERLIALLSREAGKTLSDGIAEVREAVDFC 646 *********************************************************************** PP TIGR01238 143 ryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqts 200 ryya +ed+++e +G++vcispwnfplaiftGqiaaalaaGn+v+akpaeqt+ lcl|FitnessBrowser__Caulo:CCNA_00846 647 RYYAMLAEDQFGEAEILKgpvgetnslrlagRGVFVCISPWNFPLAIFTGQIAAALAAGNAVLAKPAEQTP 717 ************98765579*************************************************** PP TIGR01238 201 liaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvplia 271 lia +av+l + aG+ + + llpGrGe+vGaalts+e + Gv+ftG t++a +in++la r+ + vp+ia lcl|FitnessBrowser__Caulo:CCNA_00846 718 LIAFEAVKLYHAAGLDPRLLALLPGRGETVGAALTSHEDLDGVAFTGGTDTAWRINQTLAARQGPIVPFIA 788 *********************************************************************** PP TIGR01238 272 etGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlt 342 etGG n m vd+ta eqv+ dv+ saf saGqrcsalr+l++ +d ad++++ +kGamd l++g p + lcl|FitnessBrowser__Caulo:CCNA_00846 789 ETGGLNGMFVDTTAQREQVIDDVIVSAFGSAGQRCSALRLLFLPHDTADHIIEGLKGAMDALVLGDPALAV 859 *********************************************************************** PP TIGR01238 343 tdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvv 413 tdvGpvidaeak+ l +h+ ++k+ ak ++ + + gtf ap+l e+ d l++evfGpvlhvv lcl|FitnessBrowser__Caulo:CCNA_00846 860 TDVGPVIDAEAKDALDKHLVRLKSDAKVLHALAAPA-----GGTFFAPVLAEIPTADFLEREVFGPVLHVV 925 ****************************99998777.....8***************************** PP TIGR01238 414 rykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGp 484 ryk ++l+kv + a+ ygltlG+hsrie+ + +++ + +Gn yvnr + GavvGvqpfGGeGlsGtGp lcl|FitnessBrowser__Caulo:CCNA_00846 926 RYKPENLEKVAGALAARRYGLTLGIHSRIESFAADVQRLVPAGNAYVNRSMTGAVVGVQPFGGEGLSGTGP 996 *********************************************************************** PP TIGR01238 485 kaGGplylyrlt 496 kaGGp+ l r+ lcl|FitnessBrowser__Caulo:CCNA_00846 997 KAGGPHALLRFA 1008 ********9996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1029 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: 00:00:00.03 # Mc/sec: 15.73 // [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