Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Ac3H11_4835 Malate synthase G (EC 2.3.3.9)
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_4835
Length = 754
Score = 958 bits (2477), Expect = 0.0
Identities = 466/733 (63%), Positives = 590/733 (80%), Gaps = 12/733 (1%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MT+R + GLQVA L+ F+ ++ +PGTGV AFW G D+++ DLAP+N ALLA+RD L
Sbjct: 19 MTDRTPIHGLQVATSLFRFIEDKVLPGTGVGGEAFWKGFDAIVADLAPRNIALLAERDRL 78
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
Q ++D WH+A G + VAY+SFL++IGYL+P+ D +ATT NVD+E+A AGPQLVVP
Sbjct: 79 QTELDTWHKANPGPIQNMVAYRSFLEKIGYLVPQPADVKATTANVDDELATQAGPQLVVP 138
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
I+NAR+ALNAANARWGSLYDALYGTDAI E DGA KG GYN +RG KVIA+AR L++ A
Sbjct: 139 ILNARYALNAANARWGSLYDALYGTDAIPETDGAEKGKGYNPVRGAKVIAFARQVLDDTA 198
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL +GSH DSTGY++EGG+LVVSL +GSTTGLK+ +Q +G+QG A+AP +VLL++NG+H
Sbjct: 199 PLASGSHKDSTGYKVEGGQLVVSLANGSTTGLKDASQFKGYQGNAAAPSSVLLQHNGLHL 258
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
+IQID ++PIGQ+DAAGV D+++E+AL+TI+D EDS+AAVDA+DK + Y NWLG+++ L
Sbjct: 259 DIQIDRSTPIGQSDAAGVSDLVLEAALSTILDLEDSVAAVDAEDKVLGYSNWLGIIQATL 318
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAIL--DKEG- 357
E++ KGGK ITR +N DR+YT G GE+ LHGRSL+F+RNVGHLMTN AIL D +G
Sbjct: 319 TEQVAKGGKTITRGLNGDRIYTGPTG-GEVRLHGRSLMFLRNVGHLMTNPAILWTDAQGT 377
Query: 358 -NEVPEGIMDGLFTSLIAVHNLNGNTSR--KNTRTGSMYIVKPKMHGPEEVAFATELFGR 414
E+PEGIMD + T+ IA+H+L G+ + +N+R GS+YIVKPKMHGP EV FA ELFGR
Sbjct: 378 QREIPEGIMDAVVTTAIALHDLQGHGANGIRNSRKGSVYIVKPKMHGPAEVGFAAELFGR 437
Query: 415 VEDVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAG 474
VE +LGLP +T+K+GIMDEERRT++NLKACI A RV FINTGFLDRTGDE+HT+M AG
Sbjct: 438 VEKLLGLPDSTVKLGIMDEERRTSVNLKACIAAASSRVAFINTGFLDRTGDEMHTAMHAG 497
Query: 475 PMVRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMA 534
PMVRK MK WI +YE NNV VGL+CGL+GKAQIGKGMWAMPDLMA ML+QK+ HP A
Sbjct: 498 PMVRKGDMKTSAWIQSYEKNNVLVGLSCGLRGKAQIGKGMWAMPDLMAEMLKQKIAHPKA 557
Query: 535 GANTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDD-----ILTIPLAQDTNWS 589
GANTAWVPSPT ATLHA+HYH++ V Q+EL K + + D +LT+P+A NWS
Sbjct: 558 GANTAWVPSPTGATLHALHYHQVKVSDIQIELEKTDVNAERDNLLTGLLTVPVAAAPNWS 617
Query: 590 EEEKRNELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRH 649
+ EK+ ELDNN+QGILGY+VRWV+QGVGCSKVPDI+++ LMEDRATLRISSQH+ANW+ H
Sbjct: 618 DAEKQQELDNNAQGILGYVVRWVDQGVGCSKVPDIHNVGLMEDRATLRISSQHLANWLHH 677
Query: 650 GVVTKDQVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYT 709
GVVT+ QV + +RMA VVD QN GDPLY+PMA +F S+A++AA +LV +G +QP+GYT
Sbjct: 678 GVVTEAQVRATFERMAAVVDGQNAGDPLYQPMAGNFGTSMAYKAACDLVFKGMEQPSGYT 737
Query: 710 EPVLHRRRREFKA 722
EP+LH R + KA
Sbjct: 738 EPLLHAWRLKLKA 750
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: 1569
Number of extensions: 71
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: 754
Length adjustment: 40
Effective length of query: 686
Effective length of database: 714
Effective search space: 489804
Effective search space used: 489804
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 Ac3H11_4835 (Malate synthase G (EC 2.3.3.9))
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.23564.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 1198.3 0.0 0 1198.1 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 Malate synthase G (EC 2.3.3.9)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 Malate synthase G (EC 2.3.3.9)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1198.1 0.0 0 0 6 719 .. 26 750 .. 21 752 .. 0.97
Alignments for each domain:
== domain 1 score: 1198.1 bits; conditional E-value: 0
TIGR01345 6 grlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhr 67
+lqva+ l +f+e++vlpgtgv e+fw+gfd+iv dlap+n lla+rd++q+ +d +h+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 26 HGLQVATSLFRFIEDKVLPGTGVGGEAFWKGFDAIVADLAPRNIALLAERDRLQTELDTWHK 87
689*********************************************************** PP
TIGR01345 68 knkgvi.dkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaa 128
n+g+i + ay+sfl++igylv++p v+ +t nvd+e+a+qagpqlvvp+lnaryalnaa
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 88 ANPGPIqNMVAYRSFLEKIGYLVPQPADVKATTANVDDELATQAGPQLVVPILNARYALNAA 149
***7761578**************************************************** PP
TIGR01345 129 narwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvky 190
narwgslydalyg+++ipe+dgaekgk ynp+rg kvi+far+ ld++ pl sgs++d y
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 150 NARWGSLYDALYGTDAIPETDGAEKGKGYNPVRGAKVIAFARQVLDDTAPLASGSHKDSTGY 211
************************************************************** PP
TIGR01345 191 kivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadk 252
k+ ++l+v l +g++t lkd +qf+gy+g+aa+p+ +ll++nglh+++qid pig++d
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 212 KVEGGQLVVSLANGSTTGLKDASQFKGYQGNAAAPSSVLLQHNGLHLDIQIDRSTPIGQSDA 273
************************************************************** PP
TIGR01345 253 akvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklne 314
a+v d+vle+a++tild+edsvaavdaedkvl+y+n+lg+ + tl e++ k g++i+r ln
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 274 AGVSDLVLEAALSTILDLEDSVAAVDAEDKVLGYSNWLGIIQATLTEQVAKGGKTITRGLNG 335
************************************************************** PP
TIGR01345 315 drsytaangeelslhgrsllfvrnvghlmtipviltde..g..eeipegildgvltsvialy 372
dr yt++ g e+ lhgrsl+f+rnvghlmt+p+il + g eipegi+d+v+t++ial+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 336 DRIYTGPTGGEVRLHGRSLMFLRNVGHLMTNPAILWTDaqGtqREIPEGIMDAVVTTAIALH 397
********************************9964431233369***************** PP
TIGR01345 373 dlkvq..nklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerr 432
dl+ + n +rnsrkgsvyivkpkmhgp ev fa +lf+r+e+llgl+ t+k+g+mdeerr
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 398 DLQGHgaNGIRNSRKGSVYIVKPKMHGPAEVGFAAELFGRVEKLLGLPDSTVKLGIMDEERR 459
**97522679**************************************************** PP
TIGR01345 433 tslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaa 494
ts+nlkacia + rvafintgfldrtgde+ht+m ag+mvrk+dmk+++w+++ye+nnv+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 460 TSVNLKACIAAASSRVAFINTGFLDRTGDEMHTAMHAGPMVRKGDMKTSAWIQSYEKNNVLV 521
************************************************************** PP
TIGR01345 495 gltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvq 556
gl cglrgkaqigkgmwampdlmaeml++k+ ++agantawvpspt+atlhalhyh+v+v
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 522 GLSCGLRGKAQIGKGMWAMPDLMAEMLKQKIAHPKAGANTAWVPSPTGATLHALHYHQVKVS 583
************************************************************** PP
TIGR01345 557 kvqkeladaerraelke....iltipvaentnwseeeikeeldnnvqgilgyvvrwveqgig 614
+q el +++ +ae+++ +lt+pva + nws+ e+++eldnn+qgilgyvvrwv+qg+g
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 584 DIQIELEKTDVNAERDNlltgLLTVPVAAAPNWSDAEKQQELDNNAQGILGYVVRWVDQGVG 645
*************97762222578************************************** PP
TIGR01345 615 cskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayr 676
cskvpdihnv lmedratlrissqhlanwl hg+v+ qv +++erma vvd qnagd+ y+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 646 CSKVPDIHNVGLMEDRATLRISSQHLANWLHHGVVTEAQVRATFERMAAVVDGQNAGDPLYQ 707
************************************************************** PP
TIGR01345 677 pmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
pma+n+ +s+a+kaa dl++kg++qpsgytep+lha+rl+ k+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 708 PMAGNFGTSMAYKAACDLVFKGMEQPSGYTEPLLHAWRLKLKA 750
****************************************997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (754 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: 8.17
//
[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