Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF353 Psest_0354 malate synthase G
Query= reanno::psRCH2:GFF353 (726 letters) >FitnessBrowser__psRCH2:GFF353 Length = 726 Score = 1449 bits (3751), Expect = 0.0 Identities = 726/726 (100%), Positives = 726/726 (100%) Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL Sbjct: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60 Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP Sbjct: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120 Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA Sbjct: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180 Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF Sbjct: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240 Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL Sbjct: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300 Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV Sbjct: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360 Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG Sbjct: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420 Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA Sbjct: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480 Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW Sbjct: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540 Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN Sbjct: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600 Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES Sbjct: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660 Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF Sbjct: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720 Query: 721 KAKNGL 726 KAKNGL Sbjct: 721 KAKNGL 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: 1800 Number of extensions: 47 Number of successful extensions: 1 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: 726 Length adjustment: 40 Effective length of query: 686 Effective length of database: 686 Effective search space: 470596 Effective search space used: 470596 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 GFF353 Psest_0354 (malate synthase G)
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.7236.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 1227.1 1.8 0 1226.9 1.8 1.0 1 lcl|FitnessBrowser__psRCH2:GFF353 Psest_0354 malate synthase G Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF353 Psest_0354 malate synthase G # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1226.9 1.8 0 0 2 721 .] 4 724 .. 3 724 .. 0.99 Alignments for each domain: == domain 1 score: 1226.9 bits; conditional E-value: 0 TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidke 76 rv++g+lqvak+l+dfv++e++pgtgvda++fw+g d +++dlap+nr llakrd++qa id++h+ + d lcl|FitnessBrowser__psRCH2:GFF353 4 RVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQAQIDAWHQARAgQAHDAV 79 789****************************************************************99557899* PP TIGR01345 77 ayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgae 152 ayksfl+eigyl +e e + +tenvd+eia agpqlvvp++nar+alnaanarwgslydalyg+++i+e dga lcl|FitnessBrowser__psRCH2:GFF353 80 AYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIMNARFALNAANARWGSLYDALYGTDAISEADGAS 155 **************************************************************************** PP TIGR01345 153 kgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevi 228 kg yn rg+kvi++ar+fl+e+ ple+gs+ d y+i +kl+v l++g++t lk+++q +g++g+a++p ++ lcl|FitnessBrowser__psRCH2:GFF353 156 KGPGYNEIRGNKVIAYARNFLNEAAPLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAV 231 **************************************************************************** PP TIGR01345 229 llktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekn 304 llk+ng+h e+qid+ pig++d a+vkdi++esa+tti+dceds+aavda+dk++vyrn+lglmkg+l e+lek lcl|FitnessBrowser__psRCH2:GFF353 232 LLKNNGIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVEELEKG 307 **************************************************************************** PP TIGR01345 305 griikrklnedrsytaange.elslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnk 379 g+ i+r +n dr+yt a+g+ el+lhgrsllf+rnvghlmt+ +il++eg+e+pegi+dg++ts+ia+++l+ + + lcl|FitnessBrowser__psRCH2:GFF353 308 GKRITRAMNPDRVYTKADGNgELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPEGIMDGLFTSLIAVHNLNGNTS 383 ******************9769****************************************************** PP TIGR01345 380 lrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgf 455 +n+r+gs+yivkpkmhgpeevafa +lf+r+ed+lgl+r+tlkvg+mdeerrt++nlkaci++++erv+fintgf lcl|FitnessBrowser__psRCH2:GFF353 384 RKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGF 459 **************************************************************************** PP TIGR01345 456 ldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlrag 531 ldrtgdeihtsmeag+mvrka mk+ w++aye+nnv+ gl cgl+gkaqigkgmwampdlma mle+k++ + ag lcl|FitnessBrowser__psRCH2:GFF353 460 LDRTGDEIHTSMEAGPMVRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAG 535 **************************************************************************** PP TIGR01345 532 antawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvr 607 antawvpsptaatlha+hyh+ dvq+ q ela+ ++a++++iltip+a++tnwseee+++eldnn qgilgy+vr lcl|FitnessBrowser__psRCH2:GFF353 536 ANTAWVPSPTAATLHAMHYHKIDVQARQVELAKR-EKASIDDILTIPLAQDTNWSEEEKRNELDNNSQGILGYMVR 610 ********************************99.7899************************************* PP TIGR01345 608 wveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnle 683 wveqg+gcskvpdi ++almedratlrissqh+anw+rhg+v+k+qv+esl+rma vvd+qn gd+ yrpma++++ lcl|FitnessBrowser__psRCH2:GFF353 611 WVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLKRMAPVVDRQNQGDPLYRPMAPDFD 686 **************************************************************************** PP TIGR01345 684 asvafkaakdlilkgtkqpsgytepilharrlefkekn 721 +svaf+aa +l+l+gtkqp+gytep+lh+rr+efk+kn lcl|FitnessBrowser__psRCH2:GFF353 687 NSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKAKN 724 ***********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (721 nodes) Target sequences: 1 (726 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06 # Mc/sec: 7.57 // [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