Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 8501453 DvMF_2183 malate synthase G (RefSeq)
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__Miya:8501453
Length = 731
Score = 930 bits (2404), Expect = 0.0
Identities = 460/731 (62%), Positives = 558/731 (76%), Gaps = 6/731 (0%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MT+RVQVGGLQ+A LYD + + PGTGVD FW ++++ +A +NRALLAKR +L
Sbjct: 1 MTQRVQVGGLQIAAPLYDVIVRDIAPGTGVDPDRFWTALENMVETMADRNRALLAKRAEL 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
Q IDAWH+ R G HD AY++FL+ IGYL+PE DF TTE VD EIA +AGPQLVVP
Sbjct: 61 QDAIDAWHRERRGTPHDGAAYEAFLRSIGYLVPEGPDFAVTTEGVDPEIALVAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISE---ADGASKGPGYNEIRGNKVIAYARNFLN 177
I NAR+ALNAANARWGSLYDALYGTD I E GA +G YN RG V+A A FL+
Sbjct: 121 ITNARYALNAANARWGSLYDALYGTDVIPEDPARGGAPRGGAYNPARGALVVARAAAFLD 180
Query: 178 EAAPLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGE-ASAPIAVLLKNN 236
EA PL TGSH D+ Y + GGKL V LKDG+ TGL +PA+ G G+ A AVLL+N+
Sbjct: 181 EAFPLATGSHADAARYDVRGGKLAVILKDGAETGLADPARFVGHAGDPAGGNGAVLLRNH 240
Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296
G+H EI+ID IG+ AAGV+D++ME+A+TTI+DCEDS+A VD DK + YRN LGL
Sbjct: 241 GLHAEIRIDREHAIGRGHAAGVRDVVMEAAMTTILDCEDSVAVVDGADKALAYRNMLGLF 300
Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356
+GDL E KGG+ + R +NPDR YT DG +L GRSLL +R VGHLMT DA+L +
Sbjct: 301 RGDLSAEFPKGGRSVLRTLNPDREYTGPDG-AAFSLPGRSLLLVRTVGHLMTTDAVLARS 359
Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416
G E+PEG++D + T+ IA+H+L G +S +N+RTG +YIVKPK HGPEEVAF ELF E
Sbjct: 360 GEEIPEGMLDTMATAYIALHDLRGTSSVRNSRTGGVYIVKPKQHGPEEVAFTVELFRMAE 419
Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476
D LG+PRNTLK+GIMDEERRTT+NLK CI+ A ERV+FINTGFLDRTGDEIHT MEAGP+
Sbjct: 420 DALGMPRNTLKIGIMDEERRTTVNLKECIRAAAERVIFINTGFLDRTGDEIHTCMEAGPV 479
Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536
VRK AM+ E+WI AYE+ NVD GLACGL G+AQ+GKGMWA PD+M M+E K+GHP AGA
Sbjct: 480 VRKNAMRGERWIIAYEDWNVDTGLACGLAGRAQVGKGMWAKPDMMREMVETKIGHPRAGA 539
Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPL-AQDTNWSEEEKRN 595
N AWVPSPTAATLHAMHYH +DV A Q LA + +A++ D+LT+PL + + +E
Sbjct: 540 NCAWVPSPTAATLHAMHYHAVDVAAVQKTLAGQRRATLADLLTLPLMGPASRPTPQEVEE 599
Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
EL NN+Q ILGY+VRWVEQG+GCSKVPDI D+ LMEDRATLRISSQH+ANW+ HG+ T+D
Sbjct: 600 ELANNAQSILGYVVRWVEQGIGCSKVPDITDVGLMEDRATLRISSQHIANWLHHGICTRD 659
Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
QVV LKRMA VVDRQN GDP YRPM+ DFD SVAFQAA +LVL G +QP+GYTEP+LH
Sbjct: 660 QVVAVLKRMAAVVDRQNAGDPAYRPMSADFDASVAFQAACDLVLLGREQPSGYTEPILHA 719
Query: 716 RRREFKAKNGL 726
RR+E KAK G+
Sbjct: 720 RRQEAKAKFGI 730
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: 1424
Number of extensions: 47
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: 731
Length adjustment: 40
Effective length of query: 686
Effective length of database: 691
Effective search space: 474026
Effective search space used: 474026
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 8501453 DvMF_2183 (malate synthase G (RefSeq))
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.1970470.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 1070.9 0.0 0 1070.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501453 DvMF_2183 malate synthase G (Ref
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501453 DvMF_2183 malate synthase G (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1070.7 0.0 0 0 1 720 [. 3 727 .. 3 728 .. 0.98
Alignments for each domain:
== domain 1 score: 1070.7 bits; conditional E-value: 0
TIGR01345 1 ervdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidke 76
+rv++g+lq+a+ l+d + +++ pgtgvd + fw++++++v+ +a +nr llakr e+q aid++hr+ + ++ d +
lcl|FitnessBrowser__Miya:8501453 3 QRVQVGGLQIAAPLYDVIVRDIAPGTGVDPDRFWTALENMVETMADRNRALLAKRAELQDAIDAWHRERRgTPHDGA 79
5799****************************************************************995679*** PP
TIGR01345 77 ayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipee...dg 150
ay+ fl+ igylv+e ++te+vd eia agpqlvvp++naryalnaanarwgslydalyg++vipe+ +g
lcl|FitnessBrowser__Miya:8501453 80 AYEAFLRSIGYLVPEGPDFAVTTEGVDPEIALVAGPQLVVPITNARYALNAANARWGSLYDALYGTDVIPEDparGG 156
*********************************************************************99644478 PP
TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaa.dpe 226
a +g+ ynp rg v++ a flde++pl +gs+ad+ +y++ +klav l++g +t l d+++fvg+ gd a
lcl|FitnessBrowser__Miya:8501453 157 APRGGAYNPARGALVVARAAAFLDEAFPLATGSHADAARYDVRGGKLAVILKDGAETGLADPARFVGHAGDPAgGNG 233
99********************************************************************9761567 PP
TIGR01345 227 villktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklek 303
++ll+++glh e++id +h ig+ a+v+d+v+e+a+ttildcedsva vd dk l yrn+lgl +g+l +++ k
lcl|FitnessBrowser__Miya:8501453 234 AVLLRNHGLHAEIRIDREHAIGRGHAAGVRDVVMEAAMTTILDCEDSVAVVDGADKALAYRNMLGLFRGDLSAEFPK 310
9**************************************************************************** PP
TIGR01345 304 ngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnkl 380
gr + r ln dr+yt+++g +sl+grsll+vr vghlmt+ ++l +geeipeg+ld++ t+ ial+dl+ +++
lcl|FitnessBrowser__Miya:8501453 311 GGRSVLRTLNPDREYTGPDGAAFSLPGRSLLLVRTVGHLMTTDAVLARSGEEIPEGMLDTMATAYIALHDLRGTSSV 387
***************************************************************************** PP
TIGR01345 381 rnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfld 457
rnsr+g vyivkpk+hgpeevaf+ +lf ed lg++r+tlk+g+mdeerrt++nlk ci ++erv+fintgfld
lcl|FitnessBrowser__Miya:8501453 388 RNSRTGGVYIVKPKQHGPEEVAFTVELFRMAEDALGMPRNTLKIGIMDEERRTTVNLKECIRAAAERVIFINTGFLD 464
***************************************************************************** PP
TIGR01345 458 rtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragant 534
rtgdeiht+meag++vrk+ m+ w+ aye nv++gl cgl g+aq+gkgmwa pd+m em+e k++ +ragan
lcl|FitnessBrowser__Miya:8501453 465 RTGDEIHTCMEAGPVVRKNAMRGERWIIAYEDWNVDTGLACGLAGRAQVGKGMWAKPDMMREMVETKIGHPRAGANC 541
***************************************************************************** PP
TIGR01345 535 awvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaent.nwseeeikeeldnnvqgilgyvvrwve 610
awvpsptaatlha+hyh vdv +vqk+la + rra+l ++lt+p+ + + + +e++eel nn+q+ilgyvvrwve
lcl|FitnessBrowser__Miya:8501453 542 AWVPSPTAATLHAMHYHAVDVAAVQKTLAGQ-RRATLADLLTLPLMGPAsRPTPQEVEEELANNAQSILGYVVRWVE 617
*****************************98.99**********9865516799*********************** PP
TIGR01345 611 qgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasva 687
qgigcskvpdi +v lmedratlrissqh+anwl hgi +++qv++ l+rma vvd+qnagd+ayrpm+ +++asva
lcl|FitnessBrowser__Miya:8501453 618 QGIGCSKVPDITDVGLMEDRATLRISSQHIANWLHHGICTRDQVVAVLKRMAAVVDRQNAGDPAYRPMSADFDASVA 694
***************************************************************************** PP
TIGR01345 688 fkaakdlilkgtkqpsgytepilharrlefkek 720
f+aa dl+l g +qpsgytepilharr+e k+k
lcl|FitnessBrowser__Miya:8501453 695 FQAACDLVLLGREQPSGYTEPILHARRQEAKAK 727
******************************987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (731 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 20.33
//
[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