Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Synpcc7942_2047 Synpcc7942_2047 glycine dehydrogenase
Query= reanno::WCS417:GFF4367 (946 letters) >FitnessBrowser__SynE:Synpcc7942_2047 Length = 953 Score = 1171 bits (3029), Expect = 0.0 Identities = 578/948 (60%), Positives = 716/948 (75%), Gaps = 12/948 (1%) Query: 9 NEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEALAKI 68 + F RH+GPR D +QML LG +SLE L A+V+P I+ L L + SEAEALA++ Sbjct: 6 HNFAQRHLGPRPADVEQMLQKLGCESLEDLLAAVVPADIRLPRSLNLPEPCSEAEALAEL 65 Query: 69 KAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQ 128 +AIA +NQ+ ++Y+GQGY NC TP I RN+LENP WYTAYTPYQ EI+QGRLEALLNFQ Sbjct: 66 RAIAHQNQILRSYLGQGYANCLTPPVIQRNILENPGWYTAYTPYQAEIAQGRLEALLNFQ 125 Query: 129 TLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQTLDVLRTRA 188 T++SDLTGL IANASLLDEATAAAEAMT ++K+K S +F + + HPQT+ V++TRA Sbjct: 126 TMVSDLTGLEIANASLLDEATAAAEAMTLSLAVAKSK-SQTYFVAHNCHPQTIAVVQTRA 184 Query: 189 EPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVAVAADLLA 248 LGI+V+V D + +P FG LLQYPA++G + DYR + E+ HA + VA DLLA Sbjct: 185 AALGIEVLVADLLQFDFQTPIFGLLLQYPATDGTIADYRSVIEQAHAQGAIATVACDLLA 244 Query: 249 LTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGK 308 LTLLTPPGEFGAD+A+G++QRFGVPLG+GGPHAA+F+TK+A+KR +PGR+VGVS D G+ Sbjct: 245 LTLLTPPGEFGADIAVGNSQRFGVPLGYGGPHAAFFATKEAYKRQIPGRIVGVSKDAQGQ 304 Query: 309 PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRVHQLTAIL 368 PALRLA+QTREQHIRR+KATSNICTAQVLLA +A YAVYHG +GLT IAR+V + T IL Sbjct: 305 PALRLALQTREQHIRRDKATSNICTAQVLLAVVAGFYAVYHGAEGLTAIARQVRRQTQIL 364 Query: 369 AKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGVSVDETTTQ 428 A+ L +LG + Q FDTL + + + A NLR + ++G+S+DETTT Sbjct: 365 AEELQSLGFKIPQQPGFDTLIVEV-EDPKVWQSRTEAAGFNLRCLSDRQLGISLDETTTD 423 Query: 429 ADIETLWAIFADGKALP---DFAAQVESTLPAALLRQSPVLSHPVFNRYHSETELMRYLR 485 +D+ L +FA G++LP D A V + A RQ+P L+HPVF +YHSETEL+RY+ Sbjct: 424 SDLLDLLTVFAQGRSLPAWEDLQAAVTDEVDPAFARQTPFLTHPVFQQYHSETELLRYIH 483 Query: 486 KLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLELTSDLE 545 +L +DL+L MIPLGSCTMKLNA +EM+P++W EF +HPFAP Q+ GY +L LE Sbjct: 484 RLQSRDLSLTTAMIPLGSCTMKLNATAEMLPISWPEFNQIHPFAPLSQTQGYQQLFQQLE 543 Query: 546 AMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTNPATAN 605 + L TG+ A+SLQPNAGSQGEYAGLL I+ YHQSRG++ R ICLIP SAHGTNPA+A Sbjct: 544 SWLAEITGFAAVSLQPNAGSQGEYAGLLVIQRYHQSRGEDHRQICLIPQSAHGTNPASAV 603 Query: 606 MAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREICGIIHD 665 MAGM+VV ACD RGN+D+ DL+ KA ++ D LAALM+TYPSTHGVFEE I EIC I+H Sbjct: 604 MAGMKVVPIACDDRGNIDVSDLQQKAAQYADQLAALMVTYPSTHGVFEEAIAEICAIVHQ 663 Query: 666 NGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLTPF 725 GGQVY+DGAN+NA VGLC P +FG DV HLNLHKTFCIPHGGGGPGVGPIGV +HL PF Sbjct: 664 QGGQVYLDGANLNAQVGLCQPAQFGADVCHLNLHKTFCIPHGGGGPGVGPIGVAAHLAPF 723 Query: 726 LPGHAAMERKE------GAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYI 779 LP H + G + AAP+GSASILPI+WMYI MMG AGL +AS +AILNANYI Sbjct: 724 LPSHPLVPEANADPQALGPIAAAPWGSASILPISWMYIRMMGAAGLTQASAIAILNANYI 783 Query: 780 SRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVA 839 + RL +YP+LY G G VAHECILDLRPLK ++GI V+DVAKRL+D+GFHAPTMS+PV Sbjct: 784 ATRLAPYYPILYRGDRGFVAHECILDLRPLKRTAGIEVEDVAKRLMDYGFHAPTMSWPVL 843 Query: 840 GTLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELV-SEW 898 GTLM+EPTESES ELDRFC AMI I E+ A+ +G LD DNPLK+APH A L+ S+W Sbjct: 844 GTLMVEPTESESLAELDRFCEAMIGIYHEVDAIASGDLDPLDNPLKHAPHPADVLLQSDW 903 Query: 899 THPYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946 Y+REQA YP P E K+WP V R+DN +GDRNLVC+C + +Y+ Sbjct: 904 NRAYSREQAAYPAPWTREHKFWPVVSRIDNAYGDRNLVCSCLPMSAYS 951 Lambda K H 0.319 0.135 0.398 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: 2082 Number of extensions: 70 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: 946 Length of database: 953 Length adjustment: 44 Effective length of query: 902 Effective length of database: 909 Effective search space: 819918 Effective search space used: 819918 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: 57 (26.6 bits)
Align candidate Synpcc7942_2047 Synpcc7942_2047 (glycine dehydrogenase)
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))
# 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/TIGR00461.hmm # target sequence database: /tmp/gapView.22867.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00461 [M=939] Accession: TIGR00461 Description: gcvP: glycine 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1549.1 0.0 0 1549.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2047 Synpcc7942_2047 glycine dehydrog Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2047 Synpcc7942_2047 glycine dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1549.0 0.0 0 0 1 939 [] 11 944 .. 11 944 .. 0.99 Alignments for each domain: == domain 1 score: 1549.0 bits; conditional E-value: 0 TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69 rhlGp +a++++ml+ lG ++l++l+ +vp dirl+r+l+l+ p +e ealael++ia +n+ ++sy+ lcl|FitnessBrowser__SynE:Synpcc7942_2047 11 RHLGPRPADVEQMLQKLGCESLEDLLAAVVPADIRLPRSLNLPEPCSEAEALAELRAIAHQNQILRSYL 79 9******************************************************************** PP TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138 G+Gy + ++ppviqrn+lenpgwytaytpyq+ei+qGrleallnfqt+v+dltGle+anasllde+taa lcl|FitnessBrowser__SynE:Synpcc7942_2047 80 GQGYANCLTPPVIQRNILENPGWYTAYTPYQAEIAQGRLEALLNFQTMVSDLTGLEIANASLLDEATAA 148 ********************************************************************* PP TIGR00461 139 aeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207 aeam ls v+k+k++ ++va+++hpqt+ vv+tra +lgiev+v d ++ +++ ++G llqypatdG lcl|FitnessBrowser__SynE:Synpcc7942_2047 149 AEAMTLSLAVAKSKSQTYFVAHNCHPQTIAVVQTRAAALGIEVLVADLLQFDFQTPIFGLLLQYPATDG 217 ********************************************************************* PP TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdey 276 +i dy+++i++++ + a+ +va+dllaltlltppg++Gadi++G +qrfGvplGyGGphaaffa+k+ y lcl|FitnessBrowser__SynE:Synpcc7942_2047 218 TIADYRSVIEQAHAQGAIATVACDLLALTLLTPPGEFGADIAVGNSQRFGVPLGYGGPHAAFFATKEAY 286 ********************************************************************* PP TIGR00461 277 krklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniar 345 kr++pGrivGvskda+G++alrlalqtreqhirrdkatsnictaqvlla+va yavyhG+ Gl iar lcl|FitnessBrowser__SynE:Synpcc7942_2047 287 KRQIPGRIVGVSKDAQGQPALRLALQTREQHIRRDKATSNICTAQVLLAVVAGFYAVYHGAEGLTAIAR 355 ********************************************************************* PP TIGR00461 346 rifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdettt 414 ++ r t+ila l+ ++++ ++ fdtl vev + + + e+a+ nlr + ++gi+ldettt lcl|FitnessBrowser__SynE:Synpcc7942_2047 356 QVRRQTQILAEELQSLGFKIPQQPGFDTLIVEVEDPKV--WQSRTEAAGFNLRCLSDRQLGISLDETTT 422 *********************************99877..8999************************* PP TIGR00461 415 kedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevfnryhsetellrylhrleskdl 483 d+ldll v+a l+ + e l+ v++ +++++ r+ +l+++vf++yhsetellry+hrl+s+dl lcl|FitnessBrowser__SynE:Synpcc7942_2047 423 DSDLLDLLTVFAQGRSLP-AWEDLQAAVTDEVDPAFARQTPFLTHPVFQQYHSETELLRYIHRLQSRDL 490 ************977666.5789********************************************** PP TIGR00461 484 alnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqp 552 +l+++miplGsctmklnataemlpi+wpef +ihpfap q++Gy++l+ qle+wl+eitGf a+slqp lcl|FitnessBrowser__SynE:Synpcc7942_2047 491 SLTTAMIPLGSCTMKLNATAEMLPISWPEFNQIHPFAPLSQTQGYQQLFQQLESWLAEITGFAAVSLQP 559 ********************************************************************* PP TIGR00461 553 nsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkak 621 n+G+qGeyaGl vi++yh+srge+hr+iclip+sahGtnpasa+maG+kvvp++cd+ Gnid+ dl++k lcl|FitnessBrowser__SynE:Synpcc7942_2047 560 NAGSQGEYAGLLVIQRYHQSRGEDHRQICLIPQSAHGTNPASAVMAGMKVVPIACDDRGNIDVSDLQQK 628 ********************************************************************* PP TIGR00461 622 aekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690 a +++d+laa+mvtypst+Gvfee+i e++ ivh+ GGqvyldGan+naqvGl++p+++Gadvchlnlh lcl|FitnessBrowser__SynE:Synpcc7942_2047 629 AAQYADQLAALMVTYPSTHGVFEEAIAEICAIVHQQGGQVYLDGANLNAQVGLCQPAQFGADVCHLNLH 697 ********************************************************************* PP TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmm 759 ktf+iphGGGGpg+gpigv +hlapflp + lv e ++ +++g ++aap+Gsasilpis+myi+mm lcl|FitnessBrowser__SynE:Synpcc7942_2047 698 KTFCIPHGGGGPGVGPIGVAAHLAPFLPSHPLVP--EANADPQALGPIAAAPWGSASILPISWMYIRMM 764 *****************************98865..6788999************************** PP TIGR00461 760 GaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGf 828 Ga Gl++as +ailnany+a+rl +y+il++g + vahecildlr+lk+ agie++dvakrl+dyGf lcl|FitnessBrowser__SynE:Synpcc7942_2047 765 GAAGLTQASAIAILNANYIATRLAPYYPILYRGDRGFVAHECILDLRPLKRTAGIEVEDVAKRLMDYGF 833 ********************************************************************* PP TIGR00461 829 haptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivae 897 hapt+s+pv+Gtlmveptesesl eldrf++ami i++e+da+ +G++++ dn+lk aph ++ l+ ++ lcl|FitnessBrowser__SynE:Synpcc7942_2047 834 HAPTMSWPVLGTLMVEPTESESLAELDRFCEAMIGIYHEVDAIASGDLDPLDNPLKHAPHPADVLLQSD 902 ********************************************************************* PP TIGR00461 898 wadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939 w+ +ysre+aaypap+++++kfwp v+r+d++yGdrnlvcsc lcl|FitnessBrowser__SynE:Synpcc7942_2047 903 WNRAYSREQAAYPAPWTREHKFWPVVSRIDNAYGDRNLVCSC 944 ****************************************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (939 nodes) Target sequences: 1 (953 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: 0.07u 0.04s 00:00:00.11 Elapsed: 00:00:00.10 # Mc/sec: 8.90 // [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