Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_008510302.1 BIBO1_RS16940 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::azobra:AZOBR_RS23695 (1235 letters) >NCBI__GCF_000182725.1:WP_008510302.1 Length = 1227 Score = 1620 bits (4194), Expect = 0.0 Identities = 849/1226 (69%), Positives = 971/1226 (79%), Gaps = 13/1226 (1%) Query: 14 EAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLIT 73 + A F +FAPPIR + LR AITAAYRRPE EC+ L EQA+LP +TARKLI Sbjct: 9 KVAVFQNFAPPIREQSALRQAITAAYRRPEAECVSALAEQATLPEETRQQIRSTARKLIE 68 Query: 74 ALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAH 133 ALRAK +G GVEGL+HEYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKI+ GDW++H Sbjct: 69 ALRAKHKGTGVEGLVHEYSLSSQEGVALMCLAEALLRIPDMATRDALIRDKISNGDWKSH 128 Query: 134 LGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGE 193 +G G S+FVNAATWGL++TGKLT+ ++ LS+ALTRLIAR GEP+IRRGVD AMRMMGE Sbjct: 129 IGGGRSLFVNAATWGLVVTGKLTNTVNDRGLSAALTRLIARCGEPVIRRGVDMAMRMMGE 188 Query: 194 QFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTASAG 253 QFVTG+TI EAL A+T+E GFRYSYDMLGEAA TA DA RYY DY AIHAIG ASAG Sbjct: 189 QFVTGETIDEALKRAKTLEERGFRYSYDMLGEAATTAADAERYYKDYETAIHAIGRASAG 248 Query: 254 RGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRL 313 RG+Y+GPGISIKLSA+HPRY+RAQ++RVM ELLP+VKALA +AK Y+IGLNIDAEEADRL Sbjct: 249 RGIYDGPGISIKLSALHPRYTRAQSERVMGELLPKVKALAAIAKSYNIGLNIDAEEADRL 308 Query: 314 ELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAY 373 ELSLDL++SLC DPDLAGW+GIGFVVQAYGKRCP+V+DF+IDLARR+ R+M+RLVKGAY Sbjct: 309 ELSLDLLQSLCEDPDLAGWDGIGFVVQAYGKRCPFVLDFIIDLARRTKRRVMVRLVKGAY 368 Query: 374 WDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYE 433 WD+EIKRAQ+DGL DFPVYTRKV+TDVSY+ACARKLLAA + +FPQFATHNAQTLATIY Sbjct: 369 WDAEIKRAQVDGLEDFPVYTRKVHTDVSYIACARKLLAATDVIFPQFATHNAQTLATIYH 428 Query: 434 MAGSDFQVGKYEFQCLHGMGEPLYKEVVGP--LKRPCRIYAPVGTHETLLAYLVRRLLEN 491 +AG DF+ GK+EFQCLHGMGEPLY EVVGP L RP RIYAPVGTHETLLAYLVRRLLEN Sbjct: 429 LAGPDFKTGKFEFQCLHGMGEPLYDEVVGPEKLGRPARIYAPVGTHETLLAYLVRRLLEN 488 Query: 492 GANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDL 551 GANSSFVNRI D V VDEL+ADPV V R++A GA H IALP NLY R NSAG DL Sbjct: 489 GANSSFVNRIGDKNVSVDELIADPVEVVRSMAVVGARHDQIALPENLYGARR-NSAGFDL 547 Query: 552 SDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALV 611 S+E LA LS L +A WTA P +A + G ++PV NP DR DVVG+VTE +EA V Sbjct: 548 SNEVTLAELSKTLKETAGRAWTAEPQVAGAKVKGVSRPVLNPGDRNDVVGTVTEIAEADV 607 Query: 612 AEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVR 671 A+A A A +W+A P ERAA L RAAD MQ MP LLGL++REAGKS+PNAIAEVR Sbjct: 608 AKAMKAAQTATISWSAVAPTERAACLERAADIMQRDMPALLGLVMREAGKSMPNAIAEVR 667 Query: 672 EAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPA 731 EAIDFLRYY Q R R H+ LGPVVCISPWNFPLAIF+GQIAAAL AGNPVLAKPA Sbjct: 668 EAIDFLRYYAEQTR-RTLGVGHKALGPVVCISPWNFPLAIFTGQIAAALVAGNPVLAKPA 726 Query: 732 EETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQR 791 EETPLIAAE VRILH GIPA ALQLLPG G +GAALV GVMFTGSTEVARLIQ Sbjct: 727 EETPLIAAEGVRILHEGGIPADALQLLPGDGRIGAALVAAPETCGVMFTGSTEVARLIQA 786 Query: 792 QLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCL 851 QLA RLLP+G PIPLIAETGGQNAMIVDSSALAEQVV DVIASAFDSAGQRCSALR+LCL Sbjct: 787 QLASRLLPNGKPIPLIAETGGQNAMIVDSSALAEQVVFDVIASAFDSAGQRCSALRVLCL 846 Query: 852 QEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFL 911 QEDVADR L MLKGA+REL IG D+L VD+GPVI++EA+ TI HI+AMR GR VE L Sbjct: 847 QEDVADRILTMLKGALRELSIGRTDQLKVDIGPVITDEAKNTIEKHIQAMRDLGRKVEQL 906 Query: 912 PLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTF 971 PL ET +GTF+APT+IEI + +L+REVFGPVLHVVR+ RDD++ L+D IN+TGYGLTF Sbjct: 907 PLGPETQNGTFVAPTIIEIESLRDLKREVFGPVLHVVRYKRDDMENLIDDINSTGYGLTF 966 Query: 972 GLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLL 1031 GLHTR+D TI V RI GN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL RL+ Sbjct: 967 GLHTRLDETIANVADRIRVGNIYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLV 1026 Query: 1032 SRRPKGWLEFRGPDAARAAGLA-YGEWLRAKGFT--AEASRCAGYVARSAIGGGAELNGP 1088 P + R A L + WL +G A+A+R G + SA+G EL GP Sbjct: 1027 ETAP---IPPRHASVHTDAALKDFARWLGNRGMNDLAQAARDTG--SASALGLELELPGP 1081 Query: 1089 VGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAA 1148 VGERNLY LH RGRVLL+PQT GL QL AVLATGN+A +D L +L+ LP +AA Sbjct: 1082 VGERNLYALHPRGRVLLVPQTEIGLYRQLTAVLATGNTAVIDEACGLRAVLKDLPETVAA 1141 Query: 1149 RVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYD 1208 R T DW+ P A L+EGD R+ +N R+A LPGP++L QAA+ E LAA + + Y Sbjct: 1142 RAIWTGDWQADAPFAGALIEGDSARIKEVNSRIAALPGPLVLTQAASPEDLAANQ-DAYC 1200 Query: 1209 LDLLLNERSVSVNTAAAGGNASLVAM 1234 L+ LL E S S+NT AAGGNASL+A+ Sbjct: 1201 LNWLLEEVSTSINTTAAGGNASLMAI 1226 Lambda K H 0.319 0.136 0.396 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: 3636 Number of extensions: 144 Number of successful extensions: 6 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: 1235 Length of database: 1227 Length adjustment: 47 Effective length of query: 1188 Effective length of database: 1180 Effective search space: 1401840 Effective search space used: 1401840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (27.3 bits)
Align candidate WP_008510302.1 BIBO1_RS16940 (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.302764.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-224 730.9 0.6 4.6e-224 730.4 0.6 1.2 1 NCBI__GCF_000182725.1:WP_008510302.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000182725.1:WP_008510302.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 730.4 0.6 4.6e-224 4.6e-224 2 497 .. 535 1027 .. 534 1030 .. 0.98 Alignments for each domain: == domain 1 score: 730.4 bits; conditional E-value: 4.6e-224 TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72 lyg r+ns+G dl+ne +l++l++ l+++a + + a p v ak +g +pv np dr+d+vG+v+e NCBI__GCF_000182725.1:WP_008510302.1 535 LYGA-RRNSAGFDLSNEVTLAELSKTLKETAGRAWTAEPQV-AGAKVKGVSRPVLNPGDRNDVVGTVTEIA 603 8998.************************************.67788999********************* PP TIGR01238 73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 +a+v +a+++a++a wsa+ + eraa+ler+ad+++++mp+l++l++reaGk++ naiaevrea+dflr NCBI__GCF_000182725.1:WP_008510302.1 604 EADVAKAMKAAQTATISWSAVAPTERAACLERAADIMQRDMPALLGLVMREAGKSMPNAIAEVREAIDFLR 674 *********************************************************************** PP TIGR01238 144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 yya+q + +l+ +kalG+vvcispwnfplaiftGqiaaal+aGn v+akpae+t+liaa++v +l+e G NCBI__GCF_000182725.1:WP_008510302.1 675 YYAEQTRRTLGVG-HKALGPVVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPLIAAEGVRILHEGG 744 ***********98.********************************************************* PP TIGR01238 215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 +pa ++qllpG G +Gaal + + Gv+ftGstevarli+ +la+r ++ +pliaetGGqnamivd NCBI__GCF_000182725.1:WP_008510302.1 745 IPADALQLLPGDGR-IGAALVAAPETCGVMFTGSTEVARLIQAQLASRLLPNgkpIPLIAETGGQNAMIVD 814 *************9.*********************************8765555**************** PP TIGR01238 283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 s+alaeqvv dv+asafdsaGqrcsalrvlc+qedvadr+lt++kGa+ el +g+ +l+ d+Gpvi +ea NCBI__GCF_000182725.1:WP_008510302.1 815 SSALAEQVVFDVIASAFDSAGQRCSALRVLCLQEDVADRILTMLKGALRELSIGRTDQLKVDIGPVITDEA 885 *********************************************************************** PP TIGR01238 354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 k+ +++hi++m++ ++kv q+ l e+++gtfvapt++e+++l +lk+evfGpvlhvvryk+d++++++ NCBI__GCF_000182725.1:WP_008510302.1 886 KNTIEKHIQAMRDLGRKVEQLPLGP--ETQNGTFVAPTIIEIESLRDLKREVFGPVLHVVRYKRDDMENLI 954 ***********************99..9******************************************* PP TIGR01238 425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 d in++Gyglt+G+h+r +et++++ +r++vGn+y+nrn++GavvGvqpfGG+GlsGtGpkaGGplyl rl NCBI__GCF_000182725.1:WP_008510302.1 955 DDINSTGYGLTFGLHTRLDETIANVADRIRVGNIYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRL 1025 **********************************************************************9 PP TIGR01238 496 tr 497 ++ NCBI__GCF_000182725.1:WP_008510302.1 1026 VE 1027 87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1227 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 41.26 // [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