Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF5083 PS417_26040 malate synthase
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__WCS417:GFF5083
Length = 725
Score = 1229 bits (3180), Expect = 0.0
Identities = 592/726 (81%), Positives = 666/726 (91%), Gaps = 1/726 (0%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MTE VQVGGLQVAKVL+DFVNNEAIPGTG+ A FWAGAD VIHDLAPKN+ALLAKRDD
Sbjct: 1 MTEHVQVGGLQVAKVLFDFVNNEAIPGTGITADQFWAGADKVIHDLAPKNKALLAKRDDF 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
QA+ID WHQ AGQAHD VAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61 QARIDTWHQTHAGQAHDPVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN++RG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGQGYNKVRGDKVIAFARAFLDEAA 180
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL GSHVDSTGY+I GKL+VSLK GS +GL++ AQL GFQG A+ PIA+LLK+NG+HF
Sbjct: 181 PLSAGSHVDSTGYKIVDGKLIVSLKGGSNSGLRDDAQLIGFQGPAAQPIAILLKHNGLHF 240
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
EIQID ++P+GQTDAAG+KD+LME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGIKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
EE+ KGGK TR MN DRVYT +G ++TLHGRSLLF+RNVGHLMT DAILDK+GNEV
Sbjct: 301 AEEVAKGGKTFTRTMNADRVYTGVNGQ-DVTLHGRSLLFVRNVGHLMTIDAILDKDGNEV 359
Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
PEGI+DGL TSL A+H+LNGN+SRKN+RTGS+YIVKPKMHGPEE AF ELFGR+E+VL
Sbjct: 360 PEGILDGLITSLAAIHSLNGNSSRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIENVLN 419
Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAG MVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGAMVRKA 479
Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
AMKAEKWISAYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 AMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539
Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
VPSPTAA LH +HYHK+DV ARQ ELAKRE+AS+DDILTIPLA +TNWS+EE RNELDNN
Sbjct: 540 VPSPTAAALHVLHYHKVDVFARQAELAKRERASVDDILTIPLASNTNWSDEEIRNELDNN 599
Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
+QGILGY+VRW++QGVGCSKVPDIND+ LMEDRATLRISSQH+ANW+RHG+V + QV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVNEVQVMES 659
Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
LKRMAPVVDRQN GD LYRP+APDFD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNAGDKLYRPLAPDFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 719
Query: 721 KAKNGL 726
KAKNGL
Sbjct: 720 KAKNGL 725
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: 1640
Number of extensions: 49
Number of successful extensions: 2
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: 725
Length adjustment: 40
Effective length of query: 686
Effective length of database: 685
Effective search space: 469910
Effective search space used: 469910
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 GFF5083 PS417_26040 (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.3190290.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 1202.9 2.6 0 1202.7 2.6 1.0 1 FitnessBrowser__WCS417:GFF5083
Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF5083
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1202.7 2.6 0 0 2 721 .] 4 723 .. 3 723 .. 0.99
Alignments for each domain:
== domain 1 score: 1202.7 bits; conditional E-value: 0
TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkeayk 79
+v++g+lqvak+l dfv++e++pgtg+ a++fw+g d++++dlap+n+ llakrd++qa id +h+ + d ayk
FitnessBrowser__WCS417:GFF5083 4 HVQVGGLQVAKVLFDFVNNEAIPGTGITADQFWAGADKVIHDLAPKNKALLAKRDDFQARIDTWHQTHAgQAHDPVAYK 82
6899***************************************************************99557899**** PP
TIGR01345 80 sflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkeyn 158
fl++igyl +e + +t+nvd+eia agpqlvvpv+nar+alna+narwgslydalyg+++i+e dgaekg+ yn
FitnessBrowser__WCS417:GFF5083 83 AFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNASNARWGSLYDALYGTDAISEADGAEKGQGYN 161
******************************************************************************* PP
TIGR01345 159 pkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhi 237
+rg+kvi+far flde+ pl++gs+ d ykivd+kl v l+ g+ l+d++q +g++g aa+p +illk+nglh
FitnessBrowser__WCS417:GFF5083 162 KVRGDKVIAFARAFLDEAAPLSAGSHVDSTGYKIVDGKLIVSLKGGSNSGLRDDAQLIGFQGPAAQPIAILLKHNGLHF 240
******************************************************************************* PP
TIGR01345 238 elqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedr 316
e+qida p+g++d a++kd+++e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n dr
FitnessBrowser__WCS417:GFF5083 241 EIQIDASTPVGQTDAAGIKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLAEEVAKGGKTFTRTMNADR 319
******************************************************************************* PP
TIGR01345 317 sytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkm 395
+yt+ ng++++lhgrsllfvrnvghlmti +il+++g+e+pegildg++ts+ a++ l+ +++ +nsr+gsvyivkpkm
FitnessBrowser__WCS417:GFF5083 320 VYTGVNGQDVTLHGRSLLFVRNVGHLMTIDAILDKDGNEVPEGILDGLITSLAAIHSLNGNSSRKNSRTGSVYIVKPKM 398
******************************************************************************* PP
TIGR01345 396 hgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvr 474
hgpee af+n+lf+rie++l+l+r+tlkvg+mdeerrt++nlkaci+ + erv+fintgfldrtgdeihtsmeagamvr
FitnessBrowser__WCS417:GFF5083 399 HGPEEAAFTNELFGRIENVLNLPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGAMVR 477
******************************************************************************* PP
TIGR01345 475 kadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrv 553
ka mk+ w++aye+ nv+ gl +gl+g+aqigkgmwampdlma mle+k+ + agantawvpsptaa+lh lhyh+v
FitnessBrowser__WCS417:GFF5083 478 KAAMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAWVPSPTAAALHVLHYHKV 556
******************************************************************************* PP
TIGR01345 554 dvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedrat 632
dv++ q+ela+ +ra+ ++iltip+a+ntnws+eei++eldnn+qgilgyvvrw++qg+gcskvpdi +v lmedrat
FitnessBrowser__WCS417:GFF5083 557 DVFARQAELAKR-ERASVDDILTIPLASNTNWSDEEIRNELDNNAQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRAT 634
**********99.7899************************************************************** PP
TIGR01345 633 lrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilh 711
lrissqh+anwlrhgiv qv+esl+rma vvd+qnagd+ yrp+a+++++ +af+aa +l+++gtkqp+gytep+lh
FitnessBrowser__WCS417:GFF5083 635 LRISSQHIANWLRHGIVNEVQVMESLKRMAPVVDRQNAGDKLYRPLAPDFDSNIAFQAAVELVIEGTKQPNGYTEPVLH 713
******************************************************************************* PP
TIGR01345 712 arrlefkekn 721
+rr+efk+kn
FitnessBrowser__WCS417:GFF5083 714 RRRREFKAKN 723
*******985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (721 nodes)
Target sequences: 1 (725 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 39.35
//
[ok]
This GapMind analysis is from Apr 09 2024. 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