Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_086509169.1 BZY95_RS06550 malate synthase G
Query= reanno::psRCH2:GFF353
(726 letters)
>NCBI__GCF_002151265.1:WP_086509169.1
Length = 728
Score = 966 bits (2497), Expect = 0.0
Identities = 477/729 (65%), Positives = 577/729 (79%), Gaps = 7/729 (0%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
M+ERV LQVA L F+N++A+PGTG+DA +FWAG D++ HDL PKNR LLA+R+ L
Sbjct: 1 MSERVTRHRLQVAAELDRFINDQALPGTGIDAESFWAGVDAIFHDLTPKNRELLAERERL 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
QAQ+D WH+ G D Y++FL+EIGYL+ +T NVD E+A AGPQLVVP
Sbjct: 61 QAQLDTWHRENPGPVRDMSVYRAFLEEIGYLVDAPAQVTVSTANVDREVAIQAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+ NAR+ALNAANARWGSLYDALYGTDAISE GA KG GYN RG KVIAYAR L+ AA
Sbjct: 121 VSNARYALNAANARWGSLYDALYGTDAISEEGGAEKGSGYNPKRGEKVIAYARGVLDLAA 180
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL TGSH D+ Y + G+LVVSL+ G TGLK P +L G+ G+A+ P ++LL N+G+H
Sbjct: 181 PLATGSHRDAVKYVLRDGRLVVSLEGGRETGLKEPGKLVGYSGDAANPESILLSNHGLHL 240
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
EIQIDP+ PIG+TD AGVKD+L+E+ALT IMDCEDS+AAVDA+DK VY NWLGLMKGDL
Sbjct: 241 EIQIDPSHPIGKTDPAGVKDLLVEAALTAIMDCEDSVAAVDAEDKVGVYANWLGLMKGDL 300
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
E +EKGGK TR ++ DR YT +G G LTL GRSL+F+RNVGHLMT A+LD +GNE+
Sbjct: 301 EEAIEKGGKTFTRRLHADRSYTTPEG-GSLTLPGRSLMFVRNVGHLMTTPAVLDADGNEL 359
Query: 361 PEGIMDGLFTSLIAVHNL-NGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVL 419
PEGI+DG+ TSL+A+H+L G +N+R+GS+YIVKPKMHGP+EVAF+ ELFGRVED+L
Sbjct: 360 PEGILDGIVTSLLALHDLKKGENDPRNSRSGSVYIVKPKMHGPKEVAFSNELFGRVEDLL 419
Query: 420 GLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRK 479
GL R+TLK+GIMDEERRT++NLKACI EA RVVFINTGFLDRTGDE+HT+MEAGPM+RK
Sbjct: 420 GLARDTLKMGIMDEERRTSVNLKACIAEAASRVVFINTGFLDRTGDEMHTAMEAGPMIRK 479
Query: 480 AAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTA 539
MK WI AYE NNV VGLACGL+G+AQIGKGMWAMPDLMAAMLEQK+GHP AGANTA
Sbjct: 480 GDMKNAAWIGAYERNNVLVGLACGLRGRAQIGKGMWAMPDLMAAMLEQKIGHPKAGANTA 539
Query: 540 WVPSPTAATLHAMHYHKIDVQARQVEL-AKREKA----SIDDILTIPLAQDTNWSEEEKR 594
WVPSPTAATLHA+HYH+IDV Q EL A+ E A +D +LT+P+A+ WS+E +
Sbjct: 540 WVPSPTAATLHALHYHQIDVAEIQRELEAQGEPALLEELLDKLLTVPVAERVEWSDEAIQ 599
Query: 595 NELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTK 654
ELDNN QGILGY+VRWVE GVGCSKVPDI+D+ LMEDRATLRISSQH+ANW+ HGVV
Sbjct: 600 QELDNNCQGILGYVVRWVEHGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLHHGVVDA 659
Query: 655 DQVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLH 714
++V ++L+RMA VVD QN GDP Y M+ DF S AF+AA +L+ +G QP+GYTEP+LH
Sbjct: 660 ERVQKTLERMAKVVDEQNAGDPAYTAMSADFAASTAFKAASDLIFKGRVQPSGYTEPLLH 719
Query: 715 RRRREFKAK 723
R KA+
Sbjct: 720 HWRAVHKAR 728
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: 1517
Number of extensions: 58
Number of successful extensions: 4
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: 728
Length adjustment: 40
Effective length of query: 686
Effective length of database: 688
Effective search space: 471968
Effective search space used: 471968
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 WP_086509169.1 BZY95_RS06550 (malate synthase G)
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.30249.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 1237.5 0.0 0 1237.4 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509169.1 BZY95_RS06550 malate synthase G
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509169.1 BZY95_RS06550 malate synthase G
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1237.4 0.0 0 0 2 719 .. 4 727 .. 3 728 .] 0.99
Alignments for each domain:
== domain 1 score: 1237.4 bits; conditional E-value: 0
TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk 70
rv+ rlqva++l +f+++++lpgtg+dae+fw+g+d+i +dl+p+nrella+r+++qa +d +hr+n+
lcl|NCBI__GCF_002151265.1:WP_086509169.1 4 RVTRHRLQVAAELDRFINDQALPGTGIDAESFWAGVDAIFHDLTPKNRELLAERERLQAQLDTWHRENP 72
78899**************************************************************** PP
TIGR01345 71 .gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslyda 138
+v d + y+ fl+eigylv+ p +vt+ t nvd e+a qagpqlvvpv naryalnaanarwgslyda
lcl|NCBI__GCF_002151265.1:WP_086509169.1 73 gPVRDMSVYRAFLEEIGYLVDAPAQVTVSTANVDREVAIQAGPQLVVPVSNARYALNAANARWGSLYDA 141
7789***************************************************************** PP
TIGR01345 139 lygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvt 207
lyg+++i+ee+gaekg+ ynpkrgekvi++ar ld + pl +gs++d+vky + d++l+v le g++t
lcl|NCBI__GCF_002151265.1:WP_086509169.1 142 LYGTDAISEEGGAEKGSGYNPKRGEKVIAYARGVLDLAAPLATGSHRDAVKYVLRDGRLVVSLEGGRET 210
********************************************************************* PP
TIGR01345 208 rlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaa 276
lk++ + vgy gdaa+pe ill ++glh+e+qid+ hpigk+d+a+vkd+++e+a+t+i+dcedsvaa
lcl|NCBI__GCF_002151265.1:WP_086509169.1 211 GLKEPGKLVGYSGDAANPESILLSNHGLHLEIQIDPSHPIGKTDPAGVKDLLVEAALTAIMDCEDSVAA 279
********************************************************************* PP
TIGR01345 277 vdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmti 345
vdaedkv vy n+lglmkg+l+e +ek g++++r+l drsyt+++g l+l+grsl+fvrnvghlmt+
lcl|NCBI__GCF_002151265.1:WP_086509169.1 280 VDAEDKVGVYANWLGLMKGDLEEAIEKGGKTFTRRLHADRSYTTPEGGSLTLPGRSLMFVRNVGHLMTT 348
********************************************************************* PP
TIGR01345 346 pviltdegeeipegildgvltsvialydlkv.qnklrnsrkgsvyivkpkmhgpeevafanklftried 413
p++l+ +g+e+pegildg++ts++al+dlk+ +n rnsr gsvyivkpkmhgp+evaf+n+lf+r+ed
lcl|NCBI__GCF_002151265.1:WP_086509169.1 349 PAVLDADGNELPEGILDGIVTSLLALHDLKKgENDPRNSRSGSVYIVKPKMHGPKEVAFSNELFGRVED 417
*****************************9735779********************************* PP
TIGR01345 414 llglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksap 482
llgl+r+tlk+g+mdeerrts+nlkacia+++ rv+fintgfldrtgde+ht+meag+m+rk+dmk a+
lcl|NCBI__GCF_002151265.1:WP_086509169.1 418 LLGLARDTLKMGIMDEERRTSVNLKACIAEAASRVVFINTGFLDRTGDEMHTAMEAGPMIRKGDMKNAA 486
********************************************************************* PP
TIGR01345 483 wlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyh 551
w+ ayernnv+ gl cglrg+aqigkgmwampdlma mle+k++ ++agantawvpsptaatlhalhyh
lcl|NCBI__GCF_002151265.1:WP_086509169.1 487 WIGAYERNNVLVGLACGLRGRAQIGKGMWAMPDLMAAMLEQKIGHPKAGANTAWVPSPTAATLHALHYH 555
********************************************************************* PP
TIGR01345 552 rvdvqkvqkeladaerrae....lkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcs 616
+ dv ++q el ++++ a l+++lt+pvae +ws+e i++eldnn+qgilgyvvrwve+g+gcs
lcl|NCBI__GCF_002151265.1:WP_086509169.1 556 QIDVAEIQRELEAQGEPALleelLDKLLTVPVAERVEWSDEAIQQELDNNCQGILGYVVRWVEHGVGCS 624
************9998877556678899***************************************** PP
TIGR01345 617 kvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleas 685
kvpdih+v lmedratlrissqh+anwl hg+v e+v+++lermakvvd+qnagd+ay m+ +++as
lcl|NCBI__GCF_002151265.1:WP_086509169.1 625 KVPDIHDVGLMEDRATLRISSQHIANWLHHGVVDAERVQKTLERMAKVVDEQNAGDPAYTAMSADFAAS 693
********************************************************************* PP
TIGR01345 686 vafkaakdlilkgtkqpsgytepilharrlefke 719
afkaa+dli+kg qpsgytep+lh +r k+
lcl|NCBI__GCF_002151265.1:WP_086509169.1 694 TAFKAASDLIFKGRVQPSGYTEPLLHHWRAVHKA 727
*****************************98876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (728 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.58
//
[ok]
This GapMind analysis is from Sep 24 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