Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 206126 DVU0701 malate synthase G (TIGR)
Query= reanno::psRCH2:GFF353 (726 letters) >FitnessBrowser__DvH:206126 Length = 729 Score = 873 bits (2255), Expect = 0.0 Identities = 421/728 (57%), Positives = 538/728 (73%), Gaps = 6/728 (0%) Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60 MT R++ GGL VA+ L+ + E +PGTG+ + FWAG + ++ L P+NR LLA+RD++ Sbjct: 1 MTGRIREGGLAVAEPLHRCIEREILPGTGISPSIFWAGLEELVGTLGPRNRELLARRDNM 60 Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120 QA IDAWH+ G+ HDA AY+ FL++I YLLP +D T+ VD E+A +AGPQLVVP Sbjct: 61 QAAIDAWHKEHQGRPHDAAAYRRFLEDIRYLLPAPQDLAVETQGVDPEVATIAGPQLVVP 120 Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180 + N R+ALNA NARWGSLYDALYG+D I+++DGA++G YN +RG KV+AYA FL+ Sbjct: 121 VTNPRYALNAVNARWGSLYDALYGSDVIADSDGAARGAAYNPLRGAKVVAYAAAFLDRTF 180 Query: 181 PLETGSHVDSTGYRIEGG----KLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNN 236 PL H D Y + G KL DG+ TGL +P G+ G P VLL+NN Sbjct: 181 PLAGARHADVVRYELTGPPVGRKLSALCADGTVTGLLHPDAFAGYTG-GERPTTVLLRNN 239 Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296 G+H E+Q D P+G AG+KD+++ESA+TTI+DCEDS+A VDA+DK + YRN LGL Sbjct: 240 GLHVELQFDRRHPVGAAHPAGLKDVVLESAVTTILDCEDSVATVDAEDKALAYRNLLGLF 299 Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356 +GDL +KGG+ + R + DR YT A G L GRSL+ +RNVG LMT DA+LD Sbjct: 300 RGDLETSFDKGGRSVFRRLAADRTYT-APGGAAYALPGRSLMLVRNVGLLMTTDAVLDAA 358 Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416 G E+PEGI+DGL T+ I +H+L G +N+ GS+YIVKPK+HGPEEVAF E F R+E Sbjct: 359 GQEIPEGILDGLVTACIGLHDLRGAGRHRNSGAGSVYIVKPKLHGPEEVAFVCEQFRRIE 418 Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476 D+LG+ RNTLK+G+MDEERRTT+NL CI+ A +R++FINTGFLDRTGDEIHT MEAGP+ Sbjct: 419 DILGMARNTLKMGVMDEERRTTLNLAECIRVASQRIIFINTGFLDRTGDEIHTCMEAGPV 478 Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536 VRK MKA++W+ AYE+ NVD GLA G GKAQIGKGMW PD +A M+ K HP AGA Sbjct: 479 VRKNDMKAQRWMLAYEDWNVDTGLAAGFGGKAQIGKGMWPKPDRLAEMVATKGAHPRAGA 538 Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNE 596 N AWVPSPTAATLHA+HYH++DV ARQ ELA +AS+DD+L +PL + S E R E Sbjct: 539 NCAWVPSPTAATLHALHYHEVDVFARQRELAGCHRASLDDLLALPLMGEARPSPAEVREE 598 Query: 597 LDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQ 656 L+NN+Q ILGY+VRWVE G+GCSKVPDI+D+ LMEDRATLRISSQH+ANW+RHG+ T+D+ Sbjct: 599 LENNAQSILGYVVRWVEMGIGCSKVPDIHDVGLMEDRATLRISSQHIANWLRHGICTEDE 658 Query: 657 VVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRR 716 V + + RMA VVDRQN+ +P YRPM+ D +SVAF+AA +LV EG +QPNGYTEP+LH R Sbjct: 659 VRDVMLRMATVVDRQNKDEPGYRPMSADPGSSVAFRAACDLVFEGARQPNGYTEPILHAR 718 Query: 717 RREFKAKN 724 RRE KA++ Sbjct: 719 RREVKARS 726 Lambda K H 0.316 0.133 0.386 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: 1384 Number of extensions: 55 Number of successful extensions: 5 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: 726 Length of database: 729 Length adjustment: 40 Effective length of query: 686 Effective length of database: 689 Effective search space: 472654 Effective search space used: 472654 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: 55 (25.8 bits)
Align candidate 206126 DVU0701 (malate synthase G (TIGR))
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))
# 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/TIGR01345.hmm # target sequence database: /tmp/gapView.959799.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01345 [M=721] Accession: TIGR01345 Description: malate_syn_G: malate synthase G 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 1048.0 0.0 0 1047.8 0.0 1.0 1 FitnessBrowser__DvH:206126 Domain annotation for each sequence (and alignments): >> FitnessBrowser__DvH:206126 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1047.8 0.0 0 0 3 720 .. 5 725 .. 3 726 .. 0.99 Alignments for each domain: == domain 1 score: 1047.8 bits; conditional E-value: 0 TIGR01345 3 vdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkeayksflke 84 + g+l va+ l++ +e+e+lpgtg+ fw+g++e+v l p+nrella+rd++qaaid++h++ + + d +ay+ fl++ FitnessBrowser__DvH:206126 5 IREGGLAVAEPLHRCIEREILPGTGISPSIFWAGLEELVGTLGPRNRELLARRDNMQAAIDAWHKEHQgRPHDAAAYRRFLED 87 67899*************************************************************995689*********** PP TIGR01345 85 igylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkeynpkrgekvie 167 i yl + p+ +et++vd e+a+ agpqlvvpv+n ryalna narwgslydalygs+vi++ dga +g ynp rg kv++ FitnessBrowser__DvH:206126 88 IRYLLPAPQDLAVETQGVDPEVATIAGPQLVVPVTNPRYALNAVNARWGSLYDALYGSDVIADSDGAARGAAYNPLRGAKVVA 170 *********************************************************************************** PP TIGR01345 168 farefldeslplesgsyadvvkyki....vdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhp 246 +a fld+++pl ++ +advv+y++ v +kl + +g vt l +++ f gy+g p+++ll++nglh+elq d rhp FitnessBrowser__DvH:206126 171 YAAAFLDRTFPLAGARHADVVRYELtgppVGRKLSALCADGTVTGLLHPDAFAGYTGGE-RPTTVLLRNNGLHVELQFDRRHP 252 ************************93333468999999*******************86.7********************** PP TIGR01345 247 igkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangeelslh 329 +g a +a++kd+vlesa+ttildcedsva+vdaedk l yrnllgl +g+l+ ++k gr + r+l dr+yta+ g +l+ FitnessBrowser__DvH:206126 253 VGAAHPAGLKDVVLESAVTTILDCEDSVATVDAEDKALAYRNLLGLFRGDLETSFDKGGRSVFRRLAADRTYTAPGGAAYALP 335 *********************************************************************************** PP TIGR01345 330 grsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftrie 412 grsl++vrnvg lmt+ ++l+ g+eipegildg++t+ i l+dl+ ++ rns gsvyivkpk+hgpeevaf + f rie FitnessBrowser__DvH:206126 336 GRSLMLVRNVGLLMTTDAVLDAAGQEIPEGILDGLVTACIGLHDLRGAGRHRNSGAGSVYIVKPKLHGPEEVAFVCEQFRRIE 418 *********************************************************************************** PP TIGR01345 413 dllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaag 495 d+lg++r+tlk+gvmdeerrt+lnl ci + +r++fintgfldrtgdeiht+meag++vrk+dmk+ w+ aye nv++g FitnessBrowser__DvH:206126 419 DILGMARNTLKMGVMDEERRTTLNLAECIRVASQRIIFINTGFLDRTGDEIHTCMEAGPVVRKNDMKAQRWMLAYEDWNVDTG 501 *********************************************************************************** PP TIGR01345 496 ltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltip 578 l +g+ gkaqigkgmw pd +aem+ kg +ragan awvpsptaatlhalhyh+vdv++ q ela +ra+l+++l +p FitnessBrowser__DvH:206126 502 LAAGFGGKAQIGKGMWPKPDRLAEMVATKGAHPRAGANCAWVPSPTAATLHALHYHEVDVFARQRELAGC-HRASLDDLLALP 583 ********************************************************************99.999********* PP TIGR01345 579 vaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslerm 661 + +++ s e++eel+nn+q+ilgyvvrwve gigcskvpdih+v lmedratlrissqh+anwlrhgi + ++v + + rm FitnessBrowser__DvH:206126 584 LMGEARPSPAEVREELENNAQSILGYVVRWVEMGIGCSKVPDIHDVGLMEDRATLRISSQHIANWLRHGICTEDEVRDVMLRM 666 *********************************************************************************** PP TIGR01345 662 akvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720 a vvd+qn ++ yrpm+ + +svaf+aa dl+++g++qp+gytepilharr+e k++ FitnessBrowser__DvH:206126 667 ATVVDRQNKDEPGYRPMSADPGSSVAFRAACDLVFEGARQPNGYTEPILHARRREVKAR 725 ********************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (721 nodes) Target sequences: 1 (729 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: 33.77 // [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