Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF974 PGA1_c09900 malate synthase GlcB
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__Phaeo:GFF974
Length = 710
Score = 862 bits (2228), Expect = 0.0
Identities = 427/715 (59%), Positives = 536/715 (74%), Gaps = 16/715 (2%)
Query: 10 LQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQAQIDAWHQ 69
+QVA L F+ ++A+PGTGV A AFWAG +++ + +NRALLAKR DLQ QIDAWH
Sbjct: 10 MQVADTLVSFIEDKALPGTGVTADAFWAGLAGLVNGMGDENRALLAKRADLQGQIDAWHI 69
Query: 70 ARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIMNARFALN 129
R GQAHDA AY++FL++IGYLLPE +DF+ T+NVD+EIA + GPQLVVPI NARFALN
Sbjct: 70 ERKGQAHDATAYEAFLRDIGYLLPEGDDFEIETQNVDDEIANVPGPQLVVPITNARFALN 129
Query: 130 AANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAAPLETGSHVD 189
AANARWGSLYDALYGTDA+ + +G GY+ RG +VIA+ R FL++ PL GS D
Sbjct: 130 AANARWGSLYDALYGTDAMGDLP---EGKGYDAGRGARVIAWGRGFLDQTFPLAEGSWND 186
Query: 190 STGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHFEIQIDPASP 249
G +EGG LV +LKD AQ G++G+A+ P +LLKNNG+H I +D
Sbjct: 187 CVGLSVEGGALVPALKDA--------AQFAGYEGDAATPGKILLKNNGLHAVIVVDANGN 238
Query: 250 IGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVEELEKGGK 309
IG+ D AG+ DI++ESAL+TIMDCEDS+A VD +DK Y NWLGLMK DL EE+ KGG+
Sbjct: 239 IGKGDQAGINDIVLESALSTIMDCEDSVACVDGEDKVTAYANWLGLMKRDLAEEVTKGGE 298
Query: 310 RITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPEGIMDGLF 369
TR +N D+ +T DG+ +L L GRSLL +RNVGHLMTN A+ D G E EG +D +
Sbjct: 299 TFTRVLNDDQTFTAPDGS-DLVLKGRSLLLVRNVGHLMTNPAVRDSAGREAGEGFIDAMV 357
Query: 370 TSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLPRNTLKVG 429
T L A+H+L N+ GS+Y+VKPKMHGPEEVAF +F VED LGLPR+T+K+G
Sbjct: 358 TVLCAMHDLQAEGG--NSLHGSVYVVKPKMHGPEEVAFTDRIFTHVEDALGLPRHTVKIG 415
Query: 430 IMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKAAMKAEKWIS 489
IMDEERRT++NLK+CI+ A+ RV FINTGFLDRTGDEIHTSMEAG M+RK MK+ WI+
Sbjct: 416 IMDEERRTSVNLKSCIRAAKHRVAFINTGFLDRTGDEIHTSMEAGAMMRKGEMKSTPWIA 475
Query: 490 AYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAWVPSPTAATL 549
+YE+ NVD+GLACGL+G+AQIGKGMWAMPD M MLE K+GHP +GA AWVPSPTAATL
Sbjct: 476 SYEDRNVDIGLACGLKGRAQIGKGMWAMPDRMGEMLEAKIGHPKSGATCAWVPSPTAATL 535
Query: 550 HAMHYHKIDVQARQVEL-AKREKASIDDILTIPLAQDTNWSEEEKRNELDNNSQGILGYM 608
HA HYH+++V Q +L A + ++DD+LTIP+ Q N S+ E E++NN+QGILGY+
Sbjct: 536 HATHYHRVNVHEVQDQLKAGGARGTLDDLLTIPVMQGENLSDAEIAQEIENNAQGILGYV 595
Query: 609 VRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLKRMAPVV 668
VRWV+QGVGCSKVPDI+++ LMEDRAT RISSQ +ANW+ HG+V + QV+ ++++MA VV
Sbjct: 596 VRWVDQGVGCSKVPDIHNVGLMEDRATCRISSQALANWLHHGIVDETQVMAAMQKMAAVV 655
Query: 669 DRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKAK 723
D QN D Y PMAP FD +AFQAA +LV G QP+GYTEPVLH RR E KA+
Sbjct: 656 DGQNASDASYTPMAPGFD-GIAFQAACDLVFRGRIQPSGYTEPVLHARRLELKAQ 709
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: 1475
Number of extensions: 65
Number of successful extensions: 7
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: 710
Length adjustment: 40
Effective length of query: 686
Effective length of database: 670
Effective search space: 459620
Effective search space used: 459620
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 GFF974 PGA1_c09900 (malate synthase GlcB)
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.9587.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 1066.3 0.0 0 1066.0 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF974 PGA1_c09900 malate synthase GlcB
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF974 PGA1_c09900 malate synthase GlcB
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1066.0 0.0 0 0 5 719 .. 7 708 .. 4 710 .] 0.98
Alignments for each domain:
== domain 1 score: 1066.0 bits; conditional E-value: 0
TIGR01345 5 agrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkeayks 80
++qva +l++f+e+++lpgtgv a++fw+g++ +v+ + enr llakr ++q id++h + k + d +ay+
lcl|FitnessBrowser__Phaeo:GFF974 7 RHDMQVADTLVSFIEDKALPGTGVTADAFWAGLAGLVNGMGDENRALLAKRADLQGQIDAWHIERKgQAHDATAYEA 83
568************************************************************99955789****** PP
TIGR01345 81 flkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkey 157
fl++igyl +e + +iet+nvd+eia gpqlvvp++nar+alnaanarwgslydalyg++++ + + +gk y
lcl|FitnessBrowser__Phaeo:GFF974 84 FLRDIGYLLPEGDDFEIETQNVDDEIANVPGPQLVVPITNARFALNAANARWGSLYDALYGTDAMGD---LPEGKGY 157
***************************************************************9865...678889* PP
TIGR01345 158 npkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktng 234
+ rg +vi+++r fld+++pl +gs++d v ++ + l+ lkd +qf gy+gdaa p illk+ng
lcl|FitnessBrowser__Phaeo:GFF974 158 DAGRGARVIAWGRGFLDQTFPLAEGSWNDCVGLSVEGGALVPA--------LKDAAQFAGYEGDAATPGKILLKNNG 226
********************************99999988755........6699********************** PP
TIGR01345 235 lhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrk 311
lh + +da+++igk d+a+++divlesa++ti+dcedsva vd edkv y n+lglmk +l e+++k g +++r
lcl|FitnessBrowser__Phaeo:GFF974 227 LHAVIVVDANGNIGKGDQAGINDIVLESALSTIMDCEDSVACVDGEDKVTAYANWLGLMKRDLAEEVTKGGETFTRV 303
***************************************************************************** PP
TIGR01345 312 lnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsv 388
ln+d+++ta++g++l+l+grsll+vrnvghlmt+p+++++ g e eg +d+++t ++a++dl+ ++ ns +gsv
lcl|FitnessBrowser__Phaeo:GFF974 304 LNDDQTFTAPDGSDLVLKGRSLLLVRNVGHLMTNPAVRDSAGREAGEGFIDAMVTVLCAMHDLQAEG--GNSLHGSV 378
*****************************************************************88..9******* PP
TIGR01345 389 yivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeiht 465
y+vkpkmhgpeevaf++++ft +ed lgl+rht+k+g+mdeerrts+nlk+ci +k+rvafintgfldrtgdeiht
lcl|FitnessBrowser__Phaeo:GFF974 379 YVVKPKMHGPEEVAFTDRIFTHVEDALGLPRHTVKIGIMDEERRTSVNLKSCIRAAKHRVAFINTGFLDRTGDEIHT 455
***************************************************************************** PP
TIGR01345 466 smeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpspta 542
smeagam+rk++mks+pw+ +ye nv+ gl cgl+g+aqigkgmwampd m emle k++ +++ga awvpspta
lcl|FitnessBrowser__Phaeo:GFF974 456 SMEAGAMMRKGEMKSTPWIASYEDRNVDIGLACGLKGRAQIGKGMWAMPDRMGEMLEAKIGHPKSGATCAWVPSPTA 532
***************************************************************************** PP
TIGR01345 543 atlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvp 619
atlha+hyhrv+v++vq++l++ + r +l+++ltipv + n s+ ei +e++nn+qgilgyvvrwv+qg+gcskvp
lcl|FitnessBrowser__Phaeo:GFF974 533 ATLHATHYHRVNVHEVQDQLKAGGARGTLDDLLTIPVMQGENLSDAEIAQEIENNAQGILGYVVRWVDQGVGCSKVP 609
***************************************************************************** PP
TIGR01345 620 dihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlil 696
dihnv lmedrat rissq lanwl hgiv qv++++++ma vvd qna d +y pma+ ++ +af+aa dl++
lcl|FitnessBrowser__Phaeo:GFF974 610 DIHNVGLMEDRATCRISSQALANWLHHGIVDETQVMAAMQKMAAVVDGQNASDASYTPMAPGFD-GIAFQAACDLVF 685
***************************************************************8.69********** PP
TIGR01345 697 kgtkqpsgytepilharrlefke 719
+g qpsgytep+lharrle k+
lcl|FitnessBrowser__Phaeo:GFF974 686 RGRIQPSGYTEPVLHARRLELKA 708
********************997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (710 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.21
//
[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