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)
>lcl|FitnessBrowser__Miya:8501453 DvMF_2183 malate synthase G
(RefSeq)
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.2662.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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 8.38
//
[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