Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_054255670.1 BN2503_RS05615 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::Cup4G11:RR42_RS20125 (1333 letters) >NCBI__GCF_001298675.1:WP_054255670.1 Length = 1335 Score = 1492 bits (3863), Expect = 0.0 Identities = 817/1360 (60%), Positives = 971/1360 (71%), Gaps = 57/1360 (4%) Query: 3 TTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGSEG 62 +TT+G+K+DD RER++ A ++ RTPHWLIKQA+ Y++ +ERG + G G Sbjct: 2 STTIGIKVDDTLRERIRNAAHNMGRTPHWLIKQAVLQYVDALERGATTIRLT--GLGEPP 59 Query: 63 AADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARLPH 122 DGA+ QPFL FAQS+ PQ+ LRAAITAA+ RPE+EC+P LL AR Sbjct: 60 QDDGAEDAPPPPPMETAQPFLVFAQSILPQTPLRAAITAAWHRPETECLPALLPLARA-- 117 Query: 123 QQAEAALAMARTLATRL----RERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLR 178 Q AE + R LATRL R+ G+G V L+QEFSLSSQEGVALMCLAEALLR Sbjct: 118 QDAEQS-GKVRELATRLVQGLRDAPAGSG----VAALVQEFSLSSQEGVALMCLAEALLR 172 Query: 179 IPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTR 238 IPD+ATRDALIRDKIS +W+SH+G+SPS+FVNAA WGL+ TGKL +T +E LS AL+R Sbjct: 173 IPDRATRDALIRDKISKGDWKSHVGRSPSLFVNAAAWGLVLTGKLTSTSSEKSLSAALSR 232 Query: 239 IIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTE 298 +IGKGGEPLIR+GV AM+LMGEQFVTG+ I+EALAN+R YE +GFRYSYDMLGEAA T+ Sbjct: 233 VIGKGGEPLIRQGVHRAMKLMGEQFVTGQNIAEALANSRTYEKQGFRYSYDMLGEAAATD 292 Query: 299 ADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLK 358 ADAQRYL +YEQAI+AIG AS GRGI+EGPGISIKLSALHPRYSRAQ++RV+ EL R+ Sbjct: 293 ADAQRYLQAYEQAIHAIGAASNGRGIFEGPGISIKLSALHPRYSRAQYDRVMAELLPRVL 352 Query: 359 SLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVI 418 L LA+QYDIG+NIDAEEADRLE+SLDL+E LC P L GW+GIGFVVQ YQKRCP VI Sbjct: 353 RLAELAKQYDIGMNIDAEEADRLELSLDLMEALCAAPSLKGWSGIGFVVQAYQKRCPHVI 412 Query: 419 DYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLL 478 DYL+DLARRSR RLM+RLVKGAYWDSEIKRAQ+DGL GYPVYTRKVYTDVSY+ACARKLL Sbjct: 413 DYLVDLARRSRRRLMVRLVKGAYWDSEIKRAQLDGLAGYPVYTRKVYTDVSYLACARKLL 472 Query: 479 SVPDVIYPQFATHNAHTLAAIYQIA---GHNYYPGQYEFQCLHGMGEPLYDQVVGPLADG 535 PD IYPQFATHNA TLA+IY +A G +YY GQYEFQCLHGMGEPLY QV G ADG Sbjct: 473 EAPDAIYPQFATHNAQTLASIYHLAQSVGGSYYSGQYEFQCLHGMGEPLYAQVTGTAADG 532 Query: 536 KFNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQM 595 K RPCRIYAPVG+HETLLAYLVRRLLENGANTSFVNRI D ++ + ELV DPV ++ Sbjct: 533 KLARPCRIYAPVGSHETLLAYLVRRLLENGANTSFVNRIGDASVPIAELVTDPVEDALRI 592 Query: 596 HADEGALGLPHPRIAQPRTLY----GESRANSAGIDLSNEHRLASLSSALLAGTSEAVSA 651 EG LG PHPRIA P L+ +SR NS G++L++E +LASL++ALL T + A Sbjct: 593 ANQEGRLGAPHPRIALPADLFADLGAQSRPNSHGLNLAHEQQLASLAAALLYSTRQTYLA 652 Query: 652 VPLLGTEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPA 711 P A P+RNP++ D VG V EA+ +V+AA + A AAPIW TP Sbjct: 653 APPGVPLPADPSRTPGWQPLRNPAELSDTVGWVYEAAAHDVQAACERAAQAAPIWAGTPP 712 Query: 712 DVRAAALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSS 771 RA AL+RAA+L+E + Q LMG+I+REAGKT NA+AE+REAVDFLRYY AQV F + Sbjct: 713 ATRADALQRAADLLEQRSQPLMGLIMREAGKTLPNAVAEIREAVDFLRYYGAQVATQFDN 772 Query: 772 DTHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGV 831 RPLG V+ ISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPL AA V LL EAGV Sbjct: 773 AAQRPLGVVLAISPWNFPLAIFCGQVAAALAAGNTVLAKPAEQTPLTAAAMVALLHEAGV 832 Query: 832 PAGAVQLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAE 891 P A+QL+PG+GE+VGAALV +V GVMFTGSTEVARL+ R ++ RL G+ +PL+AE Sbjct: 833 PRDALQLVPGQGESVGAALVAHPQVAGVMFTGSTEVARLIARQLSTRLSPTGQAIPLVAE 892 Query: 892 TGGQNAMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDE 951 TGGQNAM+VDSSALAEQVV DV+ SAFDSAGQRCSALR+LCLQ++VADR L ML+ A+ E Sbjct: 893 TGGQNAMVVDSSALAEQVVADVLASAFDSAGQRCSALRLLCLQDDVADRTLTMLRDALQE 952 Query: 952 LTMGNPDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQAD-PNGALSAACRNGTFVS 1010 T+GNPDRL TDVGPVID EAR I HI M G+ V + + +GAL NG FV+ Sbjct: 953 WTLGNPDRLHTDVGPVIDAEARAQIEAHIARMADAGQTVTRVERTDGAL-----NGHFVA 1007 Query: 1011 PTLIELDSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHI 1070 P +IE+DS L REVFGPVLHV+RYPR LD LL IN TGYGLT G+H+RIDETI+H+ Sbjct: 1008 PAIIEIDSTSRLTREVFGPVLHVIRYPREQLDALLDGINATGYGLTFGVHSRIDETIQHL 1067 Query: 1071 VERAEVGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVR 1130 ER GNLYVNRN++GAVVGVQPFGG GLSGTGPKAGGPLYLHRL+ P + ++ Sbjct: 1068 SERIHAGNLYVNRNVIGAVVGVQPFGGMGLSGTGPKAGGPLYLHRLVH-GPANTALALLP 1126 Query: 1131 ASDTVGGADETGPVRRTLTETL-ATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLP 1189 + ++ +RR TL E AQ + CE S G S+ LP Sbjct: 1127 PTPSLSEHPALLLLRRLRQTTLPLPAPEQAQAHT--------TCEAALTTSRLGASLLLP 1178 Query: 1190 GPTGERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGS-------------QAVWVESP 1236 GPTGE N Y LLPR V L + L Q+AA LA+G+ AVW ++ Sbjct: 1179 GPTGESNRYRLLPRGPVWALPRTPLGLVAQVAAALASGNPCHMVLPQDDNGCAAVW-QAL 1237 Query: 1237 MARALFARLPKAVQSRVRLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQ 1296 A A A + + +AD G A+L GD D L C +A RPGP++ V+ Sbjct: 1238 RAAAGDAGVAWLHSAEGAALAD---GAIPVAALLFEGDGDALLQACRAVAARPGPLVRVE 1294 Query: 1297 GLAHGE----PNIAIERLLIERSLSVNTAAAGGNASLMTI 1332 L E + L E+S+S NTAAAGGNA LMT+ Sbjct: 1295 SLGSDELQAGQGYDLAALCHEQSISTNTAAAGGNAQLMTM 1334 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: 4121 Number of extensions: 175 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: 1335 Length adjustment: 49 Effective length of query: 1284 Effective length of database: 1286 Effective search space: 1651224 Effective search space used: 1651224 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 WP_054255670.1 BN2503_RS05615 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde 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.3686508.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-218 711.0 0.7 7.1e-218 710.0 0.7 1.5 1 NCBI__GCF_001298675.1:WP_054255670.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001298675.1:WP_054255670.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 710.0 0.7 7.1e-218 7.1e-218 2 497 .. 616 1115 .. 615 1118 .. 0.97 Alignments for each domain: == domain 1 score: 710.0 bits; conditional E-value: 7.1e-218 TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapi...vgekakaegeaqpvknpadrkdivGqvs 69 l +++r ns G++la e++l+sl + ll + +++ aap + ++ qp++npa+ d vG v NCBI__GCF_001298675.1:WP_054255670.1 616 LGAQSRPNSHGLNLAHEQQLASLAAALLYSTRQTYLAAPPgvpLPADPSRTPGWQPLRNPAELSDTVGWVY 686 66899*******************************998421233666778889***************** PP TIGR01238 70 eadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavd 140 ea a +vq+a + a +a+++w t+++ ra l+r+adlle++ l++l++reaGktl na+ae+reavd NCBI__GCF_001298675.1:WP_054255670.1 687 EAAAHDVQAACERAAQAAPIWAGTPPATRADALQRAADLLEQRSQPLMGLIMREAGKTLPNAVAEIREAVD 757 *********************************************************************** PP TIGR01238 141 flryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellq 211 flryy+ qv ++d+ ++++lG+v++ispwnfplaif Gq+aaalaaGntv+akpaeqt+l aa v+ll+ NCBI__GCF_001298675.1:WP_054255670.1 758 FLRYYGAQVATQFDNAAQRPLGVVLAISPWNFPLAIFCGQVAAALAAGNTVLAKPAEQTPLTAAAMVALLH 828 *********************************************************************** PP TIGR01238 212 eaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnam 279 eaGvp ++ql+pG+Ge+vGaal +++++aGv+ftGstevarli ++l+ r + +pl+aetGGqnam NCBI__GCF_001298675.1:WP_054255670.1 829 EAGVPRDALQLVPGQGESVGAALVAHPQVAGVMFTGSTEVARLIARQLSTRLSPTgqaIPLVAETGGQNAM 899 ****************************************************9887889************ PP TIGR01238 280 ivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvid 350 +vds+alaeqvvadvlasafdsaGqrcsalr+lc+q+dvadr+lt+++ a++e +g+p rl+tdvGpvid NCBI__GCF_001298675.1:WP_054255670.1 900 VVDSSALAEQVVADVLASAFDSAGQRCSALRLLCLQDDVADRTLTMLRDALQEWTLGNPDRLHTDVGPVID 970 *********************************************************************** PP TIGR01238 351 aeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeld 421 aea+ +++ahi +m + +++v++v + d + +g fvap ++e+d+ + l +evfGpvlhv+ry +++ld NCBI__GCF_001298675.1:WP_054255670.1 971 AEARAQIEAHIARMADAGQTVTRVERTD--GALNGHFVAPAIIEIDSTSRLTREVFGPVLHVIRYPREQLD 1039 **************************99..8899************************************* PP TIGR01238 422 kvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplyl 492 ++d ina+Gyglt+Gvhsri+et++++ +r+++Gn+yvnrn++GavvGvqpfGG GlsGtGpkaGGplyl NCBI__GCF_001298675.1:WP_054255670.1 1040 ALLDGINATGYGLTFGVHSRIDETIQHLSERIHAGNLYVNRNVIGAVVGVQPFGGMGLSGTGPKAGGPLYL 1110 *********************************************************************** PP TIGR01238 493 yrltr 497 +rl++ NCBI__GCF_001298675.1:WP_054255670.1 1111 HRLVH 1115 **985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1335 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 77.57 // [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