Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Ga0059261_2979 Ga0059261_2979 malate synthase (EC 2.3.3.9)
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__Korea:Ga0059261_2979
Length = 700
Score = 827 bits (2137), Expect = 0.0
Identities = 433/724 (59%), Positives = 523/724 (72%), Gaps = 26/724 (3%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MT V GL VA+ L FV +PG G+DA FW+GA ++ AP+NRALL RD L
Sbjct: 1 MTAYVTRAGLSVAEPLARFVEERVLPGPGIDADVFWSGAAAIFARFAPRNRALLDTRDSL 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
QAQIDAW +A D A ++FL+ IGYL+ + F TT +VD EIA MAGPQLVVP
Sbjct: 61 QAQIDAWCAEDPARAADPAAQEAFLRGIGYLVDQPGAFTVTTADVDAEIATMAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+NARF LNAANARWGSLYDA YGTDA+ GA++ GY+ RG +VIA A+ FL+EA
Sbjct: 121 ALNARFVLNAANARWGSLYDAFYGTDALP---GAARAGGYDAERGAQVIAAAKAFLDEAV 177
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL VD GG L L +P QL G +G++ +L ++NG+H
Sbjct: 178 PLAGMKWVD-----FAGGDLP----------LADPGQLVGTRGDS-----LLFRHNGLHI 217
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
E+ ID S IG+TD AG+ D+L+E+ALTTI+D EDSIAAVDADDK Y NWLGLM+GDL
Sbjct: 218 EVVIDRDSTIGRTDPAGIADVLLEAALTTIVDLEDSIAAVDADDKVAAYSNWLGLMRGDL 277
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
VE +KGGK +TR + DRVY + + +L L GRSLLF+RNVGHLMTN A+L +G+E
Sbjct: 278 VETFDKGGKTLTRRLAEDRVYQRPFAS-DLVLPGRSLLFVRNVGHLMTNPAVLI-DGDEA 335
Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
PEGI+D + TS IA+H+L G + +N+RTGS+YIVKPKMHGP+E AF +LF VED+LG
Sbjct: 336 PEGILDAIVTSTIALHDLKGLGTHRNSRTGSVYIVKPKMHGPDEAAFTNDLFDAVEDLLG 395
Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
L R+T+KVG+MDEERRT+ NL ACI + R+ FINTGFLDRTGDEIH+SM AGPM+ KA
Sbjct: 396 LDRHTIKVGVMDEERRTSANLAACIHAVKGRIAFINTGFLDRTGDEIHSSMRAGPMIPKA 455
Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
MKA WI AYE+ NV +GLA GL G+AQIGKGMWA PD MA MLE KVGHP +GANTAW
Sbjct: 456 EMKASSWIKAYEDRNVRIGLAHGLSGRAQIGKGMWAAPDRMAEMLEVKVGHPQSGANTAW 515
Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPL-AQDTNWSEEEKRNELDN 599
VPSPTAATLHAMHYH +DV ARQ E+A + +LTIP+ A NW+ E+ ELDN
Sbjct: 516 VPSPTAATLHAMHYHTVDVFARQREIAGETVPGLAPLLTIPVAAPGRNWTPEDVARELDN 575
Query: 600 NSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVE 659
N+QGILGY+VRW++QGVGCSKVPDINDI LMEDRATLRISSQH+ANW+ HGV T V
Sbjct: 576 NAQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHMANWLLHGVATAADVDA 635
Query: 660 SLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRRE 719
+L RMA VD QN GDPLYRPMA + S+AFQAA LV +G QPNGYTEP+LHR R E
Sbjct: 636 ALVRMAAKVDAQNAGDPLYRPMAGNEAASLAFQAARALVFDGVAQPNGYTEPLLHRFRAE 695
Query: 720 FKAK 723
KA+
Sbjct: 696 AKAR 699
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: 1403
Number of extensions: 47
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: 726
Length of database: 700
Length adjustment: 39
Effective length of query: 687
Effective length of database: 661
Effective search space: 454107
Effective search space used: 454107
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 Ga0059261_2979 Ga0059261_2979 (malate synthase (EC 2.3.3.9))
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.31738.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
5.4e-308 1009.4 0.0 5.9e-307 1005.9 0.0 1.9 1 lcl|FitnessBrowser__Korea:Ga0059261_2979 Ga0059261_2979 malate synthase (
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2979 Ga0059261_2979 malate synthase (EC 2.3.3.9)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1005.9 0.0 5.9e-307 5.9e-307 2 719 .. 4 698 .. 3 700 .] 0.97
Alignments for each domain:
== domain 1 score: 1005.9 bits; conditional E-value: 5.9e-307
TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk 70
+v+ ++l va+ l +fvee+vlpg g+da+ fwsg ++i +ap+nr ll rd +qa id++ +++
lcl|FitnessBrowser__Korea:Ga0059261_2979 4 YVTRAGLSVAEPLARFVEERVLPGPGIDADVFWSGAAAIFARFAPRNRALLDTRDSLQAQIDAWCAEDP 72
678899************************************************************999 PP
TIGR01345 71 .gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslyda 138
+ d +a + fl+ igylv++p + t++t +vd+eia+ agpqlvvp+lnar+ lnaanarwgslyda
lcl|FitnessBrowser__Korea:Ga0059261_2979 73 aRAADPAAQEAFLRGIGYLVDQPGAFTVTTADVDAEIATMAGPQLVVPALNARFVLNAANARWGSLYDA 141
6789***************************************************************** PP
TIGR01345 139 lygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvt 207
+yg++++p ga +++ y+ +rg +vi+ a+ flde++pl + + d + g
lcl|FitnessBrowser__Korea:Ga0059261_2979 142 FYGTDALP---GAARAGGYDAERGAQVIAAAKAFLDEAVPLAGMKWVDF---A------------GGDL 192
*******9...4566679***********************99876553...2............4456 PP
TIGR01345 208 rlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaa 276
l d+ q vg rgd +l+++nglhie+ id ig++d+a++ d++le+a+tti+d+eds+aa
lcl|FitnessBrowser__Korea:Ga0059261_2979 193 PLADPGQLVGTRGDS-----LLFRHNGLHIEVVIDRDSTIGRTDPAGIADVLLEAALTTIVDLEDSIAA 256
6899*********85.....79*********************************************** PP
TIGR01345 277 vdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmti 345
vda+dkv+ y+n+lglm+g+l e+++k g++++r+l edr+y + ++l+l+grsllfvrnvghlmt+
lcl|FitnessBrowser__Korea:Ga0059261_2979 257 VDADDKVAAYSNWLGLMRGDLVETFDKGGKTLTRRLAEDRVYQRPFASDLVLPGRSLLFVRNVGHLMTN 325
********************************************************************* PP
TIGR01345 346 pviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftriedl 414
p++l+d g+e pegild+++ts ial+dlk ++ rnsr+gsvyivkpkmhgp+e af+n lf+ +edl
lcl|FitnessBrowser__Korea:Ga0059261_2979 326 PAVLID-GDEAPEGILDAIVTSTIALHDLKGLGTHRNSRTGSVYIVKPKMHGPDEAAFTNDLFDAVEDL 393
*****9.************************************************************** PP
TIGR01345 415 lglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapw 483
lgl+rht+kvgvmdeerrts nl aci+ vk r+afintgfldrtgdeih+sm ag+m+ ka+mk+++w
lcl|FitnessBrowser__Korea:Ga0059261_2979 394 LGLDRHTIKVGVMDEERRTSANLAACIHAVKGRIAFINTGFLDRTGDEIHSSMRAGPMIPKAEMKASSW 462
********************************************************************* PP
TIGR01345 484 lkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhr 552
+kaye nv gl gl g+aqigkgmwa pd maemle k++ +++gantawvpsptaatlha+hyh
lcl|FitnessBrowser__Korea:Ga0059261_2979 463 IKAYEDRNVRIGLAHGLSGRAQIGKGMWAAPDRMAEMLEVKVGHPQSGANTAWVPSPTAATLHAMHYHT 531
********************************************************************* PP
TIGR01345 553 vdvqkvqkeladaerraelkeiltipva.entnwseeeikeeldnnvqgilgyvvrwveqgigcskvpd 620
vdv++ q e+a + + l +ltipva + nw+ e++ +eldnn+qgilgyvvrw++qg+gcskvpd
lcl|FitnessBrowser__Korea:Ga0059261_2979 532 VDVFARQREIAGE-TVPGLAPLLTIPVAaPGRNWTPEDVARELDNNAQGILGYVVRWIDQGVGCSKVPD 599
**********988.7788********973678************************************* PP
TIGR01345 621 ihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafk 689
i ++ lmedratlrissqh+anwl hg+ + +v ++l rma vd qnagd+ yrpma+n +as+af+
lcl|FitnessBrowser__Korea:Ga0059261_2979 600 INDIGLMEDRATLRISSQHMANWLLHGVATAADVDAALVRMAAKVDAQNAGDPLYRPMAGNEAASLAFQ 668
********************************************************************* PP
TIGR01345 690 aakdlilkgtkqpsgytepilharrlefke 719
aa+ l+++g+ qp+gytep+lh+ r e k+
lcl|FitnessBrowser__Korea:Ga0059261_2979 669 AARALVFDGVAQPNGYTEPLLHRFRAEAKA 698
***************************997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (700 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: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00.13
# Mc/sec: 3.80
//
[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