Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_090274943.1 BLU11_RS15565 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::ANA3:7023590 (1064 letters) >NCBI__GCF_900105005.1:WP_090274943.1 Length = 1072 Score = 1196 bits (3094), Expect = 0.0 Identities = 615/1058 (58%), Positives = 780/1058 (73%), Gaps = 9/1058 (0%) Query: 9 ASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNK 68 A E+L + NL +L + + Y+VDE+ + ELI+L+ I+++ + LV + Sbjct: 18 ADELLHPDLEQQNLQQLAQKASQYYMVDEDTLMPELIQLLDHQPAHIKQLHQSTAVLVQR 77 Query: 69 VRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGAKWD 128 VR + + +D LQQYSL+TQEG++LMCLAEALLRIPD+ TA+ALI DKLS A W Sbjct: 78 VRS--QGDAVDSLDQLLQQYSLDTQEGVLLMCLAEALLRIPDSRTAEALIRDKLSVADWK 135 Query: 129 EHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMK 188 HL +SDS+LVNASTWGL+LT +VK+D + D P +L+RLV+RLGEPV+RQ M AMK Sbjct: 136 SHLGQSDSLLVNASTWGLILTKGLVKMDPR-DDQPVPVLNRLVSRLGEPVVRQVMSHAMK 194 Query: 189 IMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITELG- 247 +MG QFVLGR + EAL N + K GYT+S+DMLGEAA TR+DA++YF Y +AI +G Sbjct: 195 LMGHQFVLGRNLPEALNNGKSLFKQGYTYSFDMLGEAARTREDAQRYFAAYLDAIERVGQ 254 Query: 248 AQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISIDAE 307 A + + P+ISIKLSALHPRYE + +RVL EL T+ +L+ AR L++ I++DAE Sbjct: 255 ANAKATAGAAAPSISIKLSALHPRYERSQRERVLKELGATLAQLVTRARELDVAITLDAE 314 Query: 308 EVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRL 367 E DRLELSL+L ++++ A KGWG LG+VVQAYSKRALPVL WLT+LA EQGDEIPVRL Sbjct: 315 EADRLELSLELLEQVYRQQA-KGWGKLGLVVQAYSKRALPVLHWLTKLAAEQGDEIPVRL 373 Query: 368 VKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQ 427 VKGAYWD+E+K AQ G YP++TRKA TD++YLACARYLL+D RG ++PQFA+HNA Sbjct: 374 VKGAYWDTEIKLAQIEGLPNYPVFTRKANTDIAYLACARYLLADINRGRLFPQFATHNAH 433 Query: 428 TVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAV-RIYAPIGAHKDLLPYLVRRL 486 T+ + MAGDR EFQRLHGMG+ LY L A A + RIYAP+GAHKDLLPYLVRRL Sbjct: 434 TIICLLAMAGDRPIEFQRLHGMGEALYKQALQLAPAGSYCRIYAPVGAHKDLLPYLVRRL 493 Query: 487 LENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLN 546 LENGAN+SFVH+LVD P+ L HPL+ L G N I LP D++G R N+KGLN Sbjct: 494 LENGANSSFVHQLVDEDVPVAQLCRHPLEALAGKANYRNTAIPLPHDLYGPQRPNAKGLN 553 Query: 547 MNIISEAEPFFAALDKFKSTQWQAGPLVNG--QTLTGEHKTVVSPFDTTQTVGQVAFADK 604 + I S+ EP A+ + QWQ GPL+ G + V SPFD Q VGQ+ + Sbjct: 554 LMINSQLEPLLQAMQPWNQHQWQGGPLLAAAINAAPGPTQAVTSPFDRQQQVGQIQWTSP 613 Query: 605 AAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGID 664 + QA+ +A AF W V RA+ L++LADLLE + EL+ALC REAGK ++DGI Sbjct: 614 EQVPQALDAAVLAFPRWNAVAVTERAACLRRLADLLEMHFAELMALCAREAGKQLKDGIA 673 Query: 665 EVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQ 724 E+REAVDFCRYYA QA++ M +P LLPGPTGE NEL+L G+GVFV ISPWNFP+AIFLGQ Sbjct: 674 EIREAVDFCRYYADQAEQKMGQPTLLPGPTGESNELYLTGKGVFVAISPWNFPVAIFLGQ 733 Query: 725 VSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERI 784 +SAA+AAGN V+AKPAEQTS+ +R ++L H+AG+P DVLQ LPG+G +G LT+D R+ Sbjct: 734 ISAAVAAGNAVLAKPAEQTSLAAHRCIELMHEAGVPRDVLQLLPGSGKELGPLLTSDPRV 793 Query: 785 GGVCFTGSTGTAKLINRTLANRE-GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSF 843 GV FTGSTGTA+ IN LA RE G + L+AETGGQNAM+VDST+ PEQVV DV+ SSF Sbjct: 794 VGVVFTGSTGTAQQINLGLAQRESGPLATLVAETGGQNAMLVDSTALPEQVVADVLESSF 853 Query: 844 TSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDA 903 SAGQRCSALRVLFLQ+DIAD+V ++L GAM EL +G+P + TDVGPVIDA A+ L A Sbjct: 854 ASAGQRCSALRVLFLQDDIADKVEELLAGAMQELKLGDPRELATDVGPVIDAQARGKLQA 913 Query: 904 HIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELA 963 H++H +Q+G+++ + +PA G FV+P A+ +DSI L EHFGP+LH++RY ++++ Sbjct: 914 HVEHYRQLGRVLAETKVPAAWSQGDFVAPVAIRLDSIDELTSEHFGPVLHIVRYASTDVM 973 Query: 964 HVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1023 V++ IN +GFGLT GI SRNEG A ++ ++ VGNVYINRN IGAVVGVQPFGG GLSG Sbjct: 974 QVVESINRSGFGLTFGIQSRNEGFAADIDKRIRVGNVYINRNMIGAVVGVQPFGGMGLSG 1033 Query: 1024 TGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1061 TGPKAGGPHYL RFVTE+TRT N AIGGNA+LL+ GD Sbjct: 1034 TGPKAGGPHYLLRFVTERTRTINTAAIGGNASLLAQGD 1071 Lambda K H 0.317 0.133 0.377 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: 2616 Number of extensions: 104 Number of successful extensions: 8 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: 1064 Length of database: 1072 Length adjustment: 45 Effective length of query: 1019 Effective length of database: 1027 Effective search space: 1046513 Effective search space used: 1046513 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 (21.6 bits) S2: 58 (26.9 bits)
Align candidate WP_090274943.1 BLU11_RS15565 (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.713895.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-217 706.8 0.1 9.2e-217 706.4 0.1 1.1 1 NCBI__GCF_900105005.1:WP_090274943.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900105005.1:WP_090274943.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 706.4 0.1 9.2e-217 9.2e-217 1 497 [. 540 1049 .. 540 1052 .. 0.99 Alignments for each domain: == domain 1 score: 706.4 bits; conditional E-value: 9.2e-217 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivg.ekakaegeaqpvknpadrkdivGqvse 70 dlyg r n++G++l ++s+l++l + ++ + ++++q p+++ + a g +q v++p dr+++vGq++ NCBI__GCF_900105005.1:WP_090274943.1 540 DLYGPQRPNAKGLNLMINSQLEPLLQAMQPWNQHQWQGGPLLAaAINAAPGPTQAVTSPFDRQQQVGQIQW 610 89****************************************944457889******************** PP TIGR01238 71 adaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdf 141 ++ ++v +a+d+av af+ w+a+ eraa+l+rladlle+h el+al+ reaGk l++ iae+reavdf NCBI__GCF_900105005.1:WP_090274943.1 611 TSPEQVPQALDAAVLAFPRWNAVAVTERAACLRRLADLLEMHFAELMALCAREAGKQLKDGIAEIREAVDF 681 *********************************************************************** PP TIGR01238 142 lryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqt 199 +ryya+q+e+++++ + + +G++v+ispwnfp+aif+Gqi+aa+aaGn+v+akpaeqt NCBI__GCF_900105005.1:WP_090274943.1 682 CRYYADQAEQKMGQPTLLPgptgesnelyltgKGVFVAISPWNFPVAIFLGQISAAVAAGNAVLAKPAEQT 752 ***************999999************************************************** PP TIGR01238 200 sliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.vpl 269 sl a r++el++eaGvp v+qllpG G+++G ltsd+r+ Gv+ftGst +a++in la+re p ++l NCBI__GCF_900105005.1:WP_090274943.1 753 SLAAHRCIELMHEAGVPRDVLQLLPGSGKELGPLLTSDPRVVGVVFTGSTGTAQQINLGLAQRESGPlATL 823 *****************************************************************99789* PP TIGR01238 270 iaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpir 340 +aetGGqnam+vdstal+eqvvadvl+s+f+saGqrcsalrvl++q+d+ad+v +l+ Gam+elk+g p + NCBI__GCF_900105005.1:WP_090274943.1 824 VAETGGQNAMLVDSTALPEQVVADVLESSFASAGQRCSALRVLFLQDDIADKVEELLAGAMQELKLGDPRE 894 *********************************************************************** PP TIGR01238 341 lttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlh 411 l tdvGpvida+a+ +l+ah+e+ ++ ++ +a+ k + ++ +g+fvap+++ ld++del e fGpvlh NCBI__GCF_900105005.1:WP_090274943.1 895 LATDVGPVIDAQARGKLQAHVEHYRQLGRVLAETKVPA--AWSQGDFVAPVAIRLDSIDELTSEHFGPVLH 963 **********************************9999..9****************************** PP TIGR01238 412 vvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGt 482 +vry + ++ +vv+ in +G+glt+G+ sr+e+ + i+kr++vGnvy+nrn++GavvGvqpfGG GlsGt NCBI__GCF_900105005.1:WP_090274943.1 964 IVRYASTDVMQVVESINRSGFGLTFGIQSRNEGFAADIDKRIRVGNVYINRNMIGAVVGVQPFGGMGLSGT 1034 *********************************************************************** PP TIGR01238 483 GpkaGGplylyrltr 497 GpkaGGp+yl r++ NCBI__GCF_900105005.1:WP_090274943.1 1035 GPKAGGPHYLLRFVT 1049 ************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1072 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: 35.32 // [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