Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate BPHYT_RS31665 BPHYT_RS31665 malate synthase
Query= reanno::psRCH2:GFF353 (726 letters) >FitnessBrowser__BFirm:BPHYT_RS31665 Length = 724 Score = 980 bits (2534), Expect = 0.0 Identities = 477/729 (65%), Positives = 592/729 (81%), Gaps = 10/729 (1%) Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60 MT+ GGLQVA L FV EA+PGTG+D+AAFW+G D+++H+LAPKNRALLA+RD L Sbjct: 1 MTQMNTRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNRALLAERDRL 60 Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120 Q ++D WH+A G D AY++FL+ IGY++P +ATT+NVD EIA AGPQLVVP Sbjct: 61 QTELDNWHRANPGPVRDLRAYRAFLEGIGYIVPAPASVKATTDNVDTEIAEQAGPQLVVP 120 Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180 + N R+ALNAANARWGSLYDALYGTDAI E GA K +N +RG VIAYAR FL++AA Sbjct: 121 LSNQRYALNAANARWGSLYDALYGTDAIPETGGAEKQKAFNPVRGAAVIAYARKFLDQAA 180 Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240 PL GSH D+T Y ++GGKLVV+LK+G T+ LK PAQ G+QGE SAP AVLLK+NG+HF Sbjct: 181 PLANGSHADATRYSVDGGKLVVTLKNG-TSELKTPAQFIGYQGEESAPSAVLLKHNGLHF 239 Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300 EIQID + IG+TD+A VKD+++E+A++TI+DCEDS+AAVDADDK ++YRNWLGLM GDL Sbjct: 240 EIQIDASDSIGRTDSAHVKDVVVEAAVSTIIDCEDSVAAVDADDKVLLYRNWLGLMTGDL 299 Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360 EE+ K GK TR +N DRVYT A+G + LHGRSLLFIRNVGHLMTN A+L K+G+E+ Sbjct: 300 TEEVTKNGKTFTRRLNADRVYTAANGTAPVVLHGRSLLFIRNVGHLMTNPAVLTKDGHEI 359 Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420 PEGI+D + T+L A+H+ + N+RTGS+YIVKPKMHGP EVAFA+ELF RVED+L Sbjct: 360 PEGILDAVITTLCALHD---RKHQLNSRTGSVYIVKPKMHGPAEVAFASELFARVEDLLK 416 Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480 LPRNT+K+GIMDEERRT++NL ACI EA ERV FINTGFLDRTGDE+H++MEAGPM+RK Sbjct: 417 LPRNTIKMGIMDEERRTSVNLLACIAEASERVAFINTGFLDRTGDEMHSAMEAGPMMRKG 476 Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540 MK+ WISAYE +NV VGL+ GL+G+AQIGKGMWAMPDLM AMLEQK+ HP AGANTAW Sbjct: 477 DMKSSAWISAYERSNVLVGLSAGLRGRAQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAW 536 Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASI-----DDILTIPLAQDTNWSEEEKRN 595 VPSPTAATLHA+HYH++DVQA Q EL + + A++ D +LTIP+ + WS++E R+ Sbjct: 537 VPSPTAATLHALHYHQVDVQAVQRELERTDYATVRDELLDGLLTIPVVAEAKWSDDEIRS 596 Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655 E+DNN+QGILGY+VRW++QGVGCSKVPDI+D+ LMEDRATLRISSQH+ANW+ HGVV ++ Sbjct: 597 EIDNNAQGILGYVVRWIDQGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLYHGVVQRE 656 Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715 V E+ KRMA VVD QN GDPLY+PMAP FD ++AF+AA LV EG +QP+GYTEP+LH+ Sbjct: 657 LVEETFKRMAKVVDEQNAGDPLYKPMAPGFD-TIAFKAAQALVFEGRQQPSGYTEPLLHK 715 Query: 716 RRREFKAKN 724 R E K ++ Sbjct: 716 FRLEVKKES 724 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: 1468 Number of extensions: 66 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: 724 Length adjustment: 40 Effective length of query: 686 Effective length of database: 684 Effective search space: 469224 Effective search space used: 469224 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 BPHYT_RS31665 BPHYT_RS31665 (malate synthase)
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.2114.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 1205.6 0.0 0 1205.4 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS31665 BPHYT_RS31665 malate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS31665 BPHYT_RS31665 malate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1205.4 0.0 0 0 3 720 .. 5 723 .. 3 724 .] 0.98 Alignments for each domain: == domain 1 score: 1205.4 bits; conditional E-value: 0 TIGR01345 3 vdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.g 71 + g+lqva++l +fve e+lpgtg+d+++fwsgfd++v++lap+nr lla+rd++q+ +d++hr n+ + lcl|FitnessBrowser__BFirm:BPHYT_RS31665 5 NTRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNRALLAERDRLQTELDNWHRANPgP 74 6789****************************************************************77 PP TIGR01345 72 vidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalyg 141 v d ay+ fl+ igy+v+ p v+ +t+nvd+eia qagpqlvvp+ n ryalnaanarwgslydalyg lcl|FitnessBrowser__BFirm:BPHYT_RS31665 75 VRDLRAYRAFLEGIGYIVPAPASVKATTDNVDTEIAEQAGPQLVVPLSNQRYALNAANARWGSLYDALYG 144 89******************************************************************** PP TIGR01345 142 snvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkd 211 +++ipe++gaek k +np+rg vi++ar+fld++ pl +gs+ad+ +y++ +kl+v+l++g + lk+ lcl|FitnessBrowser__BFirm:BPHYT_RS31665 145 TDAIPETGGAEKQKAFNPVRGAAVIAYARKFLDQAAPLANGSHADATRYSVDGGKLVVTLKNG-TSELKT 213 *************************************************************76.578*** PP TIGR01345 212 eeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaed 281 ++qf+gy+g+ ++p+++llk+nglh e+qida + ig++d a+vkd+v+e+a++ti+dcedsvaavda+d lcl|FitnessBrowser__BFirm:BPHYT_RS31665 214 PAQFIGYQGEESAPSAVLLKHNGLHFEIQIDASDSIGRTDSAHVKDVVVEAAVSTIIDCEDSVAAVDADD 283 ********************************************************************** PP TIGR01345 282 kvlvyrnllglmkgtlkeklekngriikrklnedrsytaangee.lslhgrsllfvrnvghlmtipvilt 350 kvl+yrn+lglm+g+l e+++kng++++r+ln dr+ytaang+ ++lhgrsllf+rnvghlmt+p++lt lcl|FitnessBrowser__BFirm:BPHYT_RS31665 284 KVLLYRNWLGLMTGDLTEEVTKNGKTFTRRLNADRVYTAANGTApVVLHGRSLLFIRNVGHLMTNPAVLT 353 ******************************************96599*********************** PP TIGR01345 351 degeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerh 420 ++g+eipegild+v+t+++al+d k+q nsr+gsvyivkpkmhgp evafa +lf+r+edll l+r+ lcl|FitnessBrowser__BFirm:BPHYT_RS31665 354 KDGHEIPEGILDAVITTLCALHDRKHQL---NSRTGSVYIVKPKMHGPAEVAFASELFARVEDLLKLPRN 420 ***********************99965...*************************************** PP TIGR01345 421 tlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayern 490 t+k+g+mdeerrts+nl acia++ ervafintgfldrtgde+h++meag+m+rk+dmks++w++ayer+ lcl|FitnessBrowser__BFirm:BPHYT_RS31665 421 TIKMGIMDEERRTSVNLLACIAEASERVAFINTGFLDRTGDEMHSAMEAGPMMRKGDMKSSAWISAYERS 490 ********************************************************************** PP TIGR01345 491 nvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqk 560 nv+ gl +glrg+aqigkgmwampdlm mle+k+ ++agantawvpsptaatlhalhyh+vdvq+vq lcl|FitnessBrowser__BFirm:BPHYT_RS31665 491 NVLVGLSAGLRGRAQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAWVPSPTAATLHALHYHQVDVQAVQR 560 ********************************************************************** PP TIGR01345 561 eladaerrae....lkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnval 626 el ++ + l+ +ltipv +++ws++ei+ e+dnn+qgilgyvvrw++qg+gcskvpdih+v l lcl|FitnessBrowser__BFirm:BPHYT_RS31665 561 ELERTDYATVrdelLDGLLTIPVVAEAKWSDDEIRSEIDNNAQGILGYVVRWIDQGVGCSKVPDIHDVGL 630 **99987766344567789*************************************************** PP TIGR01345 627 medratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlil 696 medratlrissqh+anwl hg+v +e v e+++rmakvvd+qnagd+ y+pma+ ++ ++afkaa+ l++ lcl|FitnessBrowser__BFirm:BPHYT_RS31665 631 MEDRATLRISSQHIANWLYHGVVQRELVEETFKRMAKVVDEQNAGDPLYKPMAPGFD-TIAFKAAQALVF 699 ********************************************************8.69********** PP TIGR01345 697 kgtkqpsgytepilharrlefkek 720 +g +qpsgytep+lh+ rle k++ lcl|FitnessBrowser__BFirm:BPHYT_RS31665 700 EGRQQPSGYTEPLLHKFRLEVKKE 723 ********************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (721 nodes) Target sequences: 1 (724 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 12.79 // [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