Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085770261.1 B1812_RS02885 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::SB2B:6938573 (1058 letters) >NCBI__GCF_002117405.1:WP_085770261.1 Length = 1018 Score = 846 bits (2185), Expect = 0.0 Identities = 484/1026 (47%), Positives = 641/1026 (62%), Gaps = 28/1026 (2%) Query: 28 YIVDEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVG-IDAFLQQYSLE 86 Y D+ L+A P A + A +LVA R +GL++G I+ FL+++SL Sbjct: 14 YAEDDAQIAARLLARRPDPGARDAT-EALARELVAASRP---QGLLIGGIEDFLREFSLT 69 Query: 87 TQEGIILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGK 146 ++EG+ +M LAE+LLR+PD ET D L+ADKL+ + H D++LV A + L L+ + Sbjct: 70 SREGLAVMALAESLLRVPDDETLDRLLADKLAVGDFAHHRIAGDALLVQACAFALGLSAR 129 Query: 147 IVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKR 206 + + +P + RLG P +R A AM++MG FV G TIE NA +R Sbjct: 130 LFEEG----ASPHGAAESVARRLGLPALRLAAKQAMRLMGAHFVFGETIE----NALSRR 181 Query: 207 KLGYTHSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPR 266 +S+DMLGEAA T +DA++Y+ YA+AI+A+G A ++ RP +S+KLSALHPR Sbjct: 182 APHLRYSFDMLGEAARTQEDAERYFEAYAHAIEAVGGAAGAQALPERPGVSVKLSALHPR 241 Query: 267 YEVANEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGW 326 YE + +RV+ EL L+ L AR ++ IDAEE DRLELSL + ++ + KGW Sbjct: 242 YEAISRERVLAELAPRLLDLARLAREHDLAFTIDAEEADRLELSLDVMARVVADPSLKGW 301 Query: 327 GLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLF 386 G+ VQAY KRA V+ + AK + LRLVKGAYWD E+K AQ+ G A YP+F Sbjct: 302 EGFGLAVQAYQKRAEAVIDHVAGWAKTLNRRLMLRLVKGAYWDLEIKRAQERGLADYPVF 361 Query: 387 TRKAATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAM-VGDRKFEFQRLHGMG 445 TRKA TD +YLACA L +E +++PQFA+HNA T AAI A FEFQRLHGMG Sbjct: 362 TRKAMTDANYLACAARLFAEP---MLFPQFATHNAMTAAAILAQGAKPESFEFQRLHGMG 418 Query: 446 QELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLV 505 + LY +L + A VR+YAP+G H+DLL YLVRRL+ENGAN+S+V +L DP IE L+ Sbjct: 419 EGLYGLLLQKGA--AVRVYAPVGKHRDLLAYLVRRLIENGANSSYVARLADPHCGIEDLL 476 Query: 506 THPLKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSA 565 P L + + + P D++ R NS G+ ++ + ++ A Sbjct: 477 EDPFAALGRPENARHRHLPLPKDLYRPLRSNSDGVEFGDQKALSALLVEIDASRGAKFFA 536 Query: 566 GPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRA 625 P T + R + SP++ T +VG V A+ A+++ A+A A +AF++W P ETRA Sbjct: 537 QPASASMT---QKRAIHSPFDGT-RVGDVIEADAASLDVAMAAAHRAFSAWGAQPAETRA 592 Query: 626 NALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELL 685 L++ A L+E R LIAL E GK++ D + EVREA D+CRYYA A+++M + L Sbjct: 593 QILERAAALIESRRGRLIALLQSEGGKTLDDALAEVREAADYCRYYANVARELM-RERAL 651 Query: 686 PGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRA 745 PGPTGE N L GRGVFVCISPWNFPLAIF+GQ+AAAL GN V AKPAEQT LIGF A Sbjct: 652 PGPTGEENRLRHVGRGVFVCISPWNFPLAIFVGQIAAALVAGNAVAAKPAEQTPLIGFEA 711 Query: 746 VQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAI 805 V L EAG+P D LQFLPG GA VGA L + E GV FTGS A+ INRALA + G I Sbjct: 712 VALLREAGVPADALQFLPGDGA-VGASLVAHELTAGVVFTGSVAVAQEINRALAKKPGPI 770 Query: 806 IPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVL 865 +PLIAETGG NAM+VDST+ E V +DV +SAF SAGQRCSALR+LYLQE+I + L + Sbjct: 771 VPLIAETGGINAMIVDSTALFEHVADDVCASAFRSAGQRCSALRLLYLQEEIFDACLATI 830 Query: 866 KGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFV 925 GA EL LG+PG T +GPVID AKA L+ ++ + G +++ + P G FV Sbjct: 831 VGAAKELRLGDPGDPATHIGPVIDRGAKAALDDYLARRRAEGSVVYTGAAP---GQGCFV 887 Query: 926 APTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALE 985 AP V + S + L +E FGP+LHV ++A ++ +I + +GLT+G+HSR E A Sbjct: 888 APHVVRLSSGRELNQEIFGPVLHVAPWRAGDFDSLVAEIMAANYGLTIGLHSRIEARAKR 947 Query: 986 VADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAI 1045 +A GN+YINR IGAVVG QPFGG LSGTGPKAGG YL RFV E T T N A+ Sbjct: 948 LAALAPAGNIYINRTMIGAVVGSQPFGGFNLSGTGPKAGGADYLRRFVREITVTTNTAAL 1007 Query: 1046 GGNATL 1051 GG+ L Sbjct: 1008 GGDLRL 1013 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: 2313 Number of extensions: 92 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: 1058 Length of database: 1018 Length adjustment: 45 Effective length of query: 1013 Effective length of database: 973 Effective search space: 985649 Effective search space used: 985649 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: 57 (26.6 bits)
Align candidate WP_085770261.1 B1812_RS02885 (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.4034767.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-169 549.0 0.6 6.2e-169 548.6 0.6 1.1 1 NCBI__GCF_002117405.1:WP_085770261.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002117405.1:WP_085770261.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.6 0.6 6.2e-169 6.2e-169 1 497 [. 499 996 .. 499 999 .. 0.97 Alignments for each domain: == domain 1 score: 548.6 bits; conditional E-value: 6.2e-169 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73 dly r+ns Gv++ ++ l l ++ ++ kf a p + + + + +p d vG v eada NCBI__GCF_002117405.1:WP_085770261.1 499 DLYRPLRSNSDGVEFGDQKALSALLVEIDASRGAKFFAQPAS----ASMTQKRAIHSPFDG-TRVGDVIEADA 566 799999********************************9987....4455667899***97.579******** PP TIGR01238 74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146 a + a+ +a +af+ w a +a+ ra iler+a l+es+ l+all+ e Gktl++a+aevrea d++ryya NCBI__GCF_002117405.1:WP_085770261.1 567 ASLDVAMAAAHRAFSAWGAQPAETRAQILERAAALIESRRGRLIALLQSEGGKTLDDALAEVREAADYCRYYA 639 ************************************************************************* PP TIGR01238 147 kqvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaarav 207 + +++ + e + +G++vcispwnfplaif+Gqiaaal+aGn+v akpaeqt+li +av NCBI__GCF_002117405.1:WP_085770261.1 640 NVARELMRERALPGptgeenrlrhvgRGVFVCISPWNFPLAIFVGQIAAALVAGNAVAAKPAEQTPLIGFEAV 712 ***998888865559999******************************************************* PP TIGR01238 208 ellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnami 280 +ll+eaGvpa ++q+lpG G+ vGa+l ++e aGv+ftGs +va+ in+alak+ + vpliaetGG nami NCBI__GCF_002117405.1:WP_085770261.1 713 ALLREAGVPADALQFLPGDGA-VGASLVAHELTAGVVFTGSVAVAQEINRALAKKPGPIVPLIAETGGINAMI 784 *********************.*************************************************** PP TIGR01238 281 vdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 vdstal e v dv asaf saGqrcsalr+l++qe++ d l i Ga +el++g p+ t +Gpvid a NCBI__GCF_002117405.1:WP_085770261.1 785 VDSTALFEHVADDVCASAFRSAGQRCSALRLLYLQEEIFDACLATIVGAAKELRLGDPGDPATHIGPVIDRGA 857 ************************************************************************* PP TIGR01238 354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdk 426 k l ++ + +a + v+ +g fvap ++ l + el++e+fGpvlhv ++a ++d++v + NCBI__GCF_002117405.1:WP_085770261.1 858 KAALDDYLARRRAEGSVVYTGAA-----PGQGCFVAPHVVRLSSGRELNQEIFGPVLHVAPWRAGDFDSLVAE 925 **********9999988886544.....559****************************************** PP TIGR01238 427 inakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 i a yglt+G+hsrie +++ a +Gn+y+nr ++GavvG qpfGG lsGtGpkaGG+ yl r++r NCBI__GCF_002117405.1:WP_085770261.1 926 IMAANYGLTIGLHSRIEARAKRLAALAPAGNIYINRTMIGAVVGSQPFGGFNLSGTGPKAGGADYLRRFVR 996 ********************************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1018 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 31.08 // [ok]
This GapMind analysis is from Apr 09 2024. 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