Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate H281DRAFT_00963 H281DRAFT_00963 malate synthase
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__Burk376:H281DRAFT_00963
Length = 723
Score = 973 bits (2516), Expect = 0.0
Identities = 479/730 (65%), Positives = 588/730 (80%), Gaps = 12/730 (1%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MT+ GGLQVA L FV EA+PGTG+D+AAFW+G D+++H+LAPKN ALLA+RD L
Sbjct: 1 MTQMNPRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNHALLAERDRL 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
Q ++D WH+A G D AY++FL+ IGY++P +ATT+ VD EIA AGPQLVVP
Sbjct: 61 QTELDNWHRANPGPVRDLRAYRAFLEGIGYIVPAPASVKATTDQVDTEIAEQAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+ N R+ALNAANARWGSLYDALYGTDAI E +GA + +N +RG VIAYAR FL+EAA
Sbjct: 121 LSNQRYALNAANARWGSLYDALYGTDAIPETNGADRQKTFNPVRGAAVIAYARKFLDEAA 180
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL GSH D+T Y +EGGKLVV+LK+G T+ LK PAQ G+QG+ASAP AVLLK+NG+HF
Sbjct: 181 PLANGSHADATRYSVEGGKLVVALKNG-TSELKTPAQFVGYQGDASAPSAVLLKHNGLHF 239
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
EIQID IG+TDAA VKD+++E+A++TI+DCEDS+AAVDADDK +YRNWLGLM GDL
Sbjct: 240 EIQIDANDSIGKTDAAHVKDVVVEAAVSTIIDCEDSVAAVDADDKVQLYRNWLGLMNGDL 299
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
EE+ K GK TR +N DRVY A+G + LHGRSLLFIRNVGHLMTN A+L K+G E+
Sbjct: 300 TEEVTKNGKTFTRRLNDDRVYVAANGTAPVVLHGRSLLFIRNVGHLMTNPAVLTKDGAEI 359
Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
PEGI+D + T+L A+H+ + N+RTGS+YIVKPKMHGP EVAFA+ELF RVED+L
Sbjct: 360 PEGILDAVMTTLCALHD---RKHKLNSRTGSIYIVKPKMHGPAEVAFASELFARVEDLLK 416
Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
LPRNT+K+GIMDEERRT++NL ACI +A ERV FINTGFLDRTGDE+H++MEAGPM+RK
Sbjct: 417 LPRNTIKMGIMDEERRTSVNLLACIAQASERVAFINTGFLDRTGDEMHSAMEAGPMMRKG 476
Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
MK+ WI+AYE +NV VGL GL+G++QIGKGMWAMPDLM AMLEQK+ HP AGANTAW
Sbjct: 477 DMKSSAWIAAYERSNVLVGLHAGLRGRSQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAW 536
Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASI-----DDILTIPLAQDTNWSEEEKRN 595
VPSPTAATLHA+HYH+IDVQA Q +L + + AS+ D +LTIP+ + NWS +E R
Sbjct: 537 VPSPTAATLHALHYHQIDVQAVQQQLERTDYASVRDELLDGLLTIPVVETANWSADEIRA 596
Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
ELDNN+QGILGY+VRW++QGVGCSKVPDI++I LMEDRATLRISSQH+ANW+ HGVVT++
Sbjct: 597 ELDNNAQGILGYVVRWIDQGVGCSKVPDIHNIGLMEDRATLRISSQHIANWLYHGVVTRE 656
Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
QV E+ KRMA VVD+QN GDP YRPMAP FD ++AF+AA LV EG +QP+GYTEP+LH+
Sbjct: 657 QVEETFKRMAQVVDQQNAGDPNYRPMAPSFD-TIAFKAAQALVFEGRQQPSGYTEPLLHK 715
Query: 716 RRREFKAKNG 725
R + KNG
Sbjct: 716 FR--LQVKNG 723
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: 1454
Number of extensions: 58
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: 723
Length adjustment: 40
Effective length of query: 686
Effective length of database: 683
Effective search space: 468538
Effective search space used: 468538
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 H281DRAFT_00963 H281DRAFT_00963 (malate synthase)
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.11508.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 1210.9 0.1 0 1210.7 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00963 H281DRAFT_00963 malate synthase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00963 H281DRAFT_00963 malate synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1210.7 0.1 0 0 5 719 .. 7 722 .. 3 723 .] 0.98
Alignments for each domain:
== domain 1 score: 1210.7 bits; conditional E-value: 0
TIGR01345 5 agrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk 70
g+lqva++l +fve e+lpgtg+d+++fwsgfd++v++lap+n+ lla+rd++q+ +d++hr n+
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 7 RGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNHALLAERDRLQTELDNWHRANP 72
689*************************************************************** PP
TIGR01345 71 .gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgsl 135
+v d ay+ fl+ igy+v+ p v+ +t++vd+eia qagpqlvvp+ n ryalnaanarwgsl
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 73 gPVRDLRAYRAFLEGIGYIVPAPASVKATTDQVDTEIAEQAGPQLVVPLSNQRYALNAANARWGSL 138
7789************************************************************** PP
TIGR01345 136 ydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavql 201
ydalyg+++ipe++ga++ k++np+rg vi++ar+flde+ pl +gs+ad+ +y++ +kl+v l
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 139 YDALYGTDAIPETNGADRQKTFNPVRGAAVIAYARKFLDEAAPLANGSHADATRYSVEGGKLVVAL 204
****************************************************************** PP
TIGR01345 202 esgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaitti 267
++g + lk+++qfvgy+gda++p+++llk+nglh e+qida++ igk+d a+vkd+v+e+a++ti
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 205 KNG-TSELKTPAQFVGYQGDASAPSAVLLKHNGLHFEIQIDANDSIGKTDAAHVKDVVVEAAVSTI 269
*76.578*********************************************************** PP
TIGR01345 268 ldcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangee.lslhgrs 332
+dcedsvaavda+dkv +yrn+lglm+g+l e+++kng++++r+ln+dr+y+aang+ ++lhgrs
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 270 IDCEDSVAAVDADDKVQLYRNWLGLMNGDLTEEVTKNGKTFTRRLNDDRVYVAANGTApVVLHGRS 335
********************************************************86599***** PP
TIGR01345 333 llfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgp 398
llf+rnvghlmt+p++lt++g eipegild+v+t+++al+d k++ nsr+gs+yivkpkmhgp
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 336 LLFIRNVGHLMTNPAVLTKDGAEIPEGILDAVMTTLCALHDRKHKL---NSRTGSIYIVKPKMHGP 398
*****************************************99854...***************** PP
TIGR01345 399 eevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeih 464
evafa +lf+r+edll l+r+t+k+g+mdeerrts+nl acia++ ervafintgfldrtgde+h
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 399 AEVAFASELFARVEDLLKLPRNTIKMGIMDEERRTSVNLLACIAQASERVAFINTGFLDRTGDEMH 464
****************************************************************** PP
TIGR01345 465 tsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlra 530
++meag+m+rk+dmks++w+ ayer+nv+ gl++glrg++qigkgmwampdlm mle+k+ ++a
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 465 SAMEAGPMMRKGDMKSSAWIAAYERSNVLVGLHAGLRGRSQIGKGMWAMPDLMHAMLEQKIAHPKA 530
****************************************************************** PP
TIGR01345 531 gantawvpsptaatlhalhyhrvdvqkvqkeladaerrae....lkeiltipvaentnwseeeike 592
gantawvpsptaatlhalhyh+ dvq+vq++l ++ + l+ +ltipv e++nws++ei++
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 531 GANTAWVPSPTAATLHALHYHQIDVQAVQQQLERTDYASVrdelLDGLLTIPVVETANWSADEIRA 596
*********************************9987766344566789***************** PP
TIGR01345 593 eldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvlesl 658
eldnn+qgilgyvvrw++qg+gcskvpdihn+ lmedratlrissqh+anwl hg+v++eqv e++
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 597 ELDNNAQGILGYVVRWIDQGVGCSKVPDIHNIGLMEDRATLRISSQHIANWLYHGVVTREQVEETF 662
****************************************************************** PP
TIGR01345 659 ermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
+rma+vvd+qnagd+ yrpma+ ++ ++afkaa+ l+++g +qpsgytep+lh+ rl+ k+
lcl|FitnessBrowser__Burk376:H281DRAFT_00963 663 KRMAQVVDQQNAGDPNYRPMAPSFD-TIAFKAAQALVFEGRQQPSGYTEPLLHKFRLQVKN 722
************************8.69*****************************9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (723 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 10.75
//
[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