Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF974 PGA1_c09900 malate synthase GlcB
Query= reanno::psRCH2:GFF353
(726 letters)
>lcl|FitnessBrowser__Phaeo:GFF974 PGA1_c09900 malate synthase GlcB
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.31530.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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 7.79
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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