Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate PfGW456L13_1139 Malate synthase G (EC 2.3.3.9)
Query= reanno::psRCH2:GFF353
(726 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139
Length = 725
Score = 1236 bits (3198), Expect = 0.0
Identities = 600/726 (82%), Positives = 667/726 (91%), Gaps = 1/726 (0%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MTE VQVGGLQVAKVL+DFVNNEAIPGTG+ A FWAGAD VIHDLAPKN+ALLAKRDD
Sbjct: 1 MTEHVQVGGLQVAKVLFDFVNNEAIPGTGLTADKFWAGADKVIHDLAPKNKALLAKRDDF 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
QA+IDAWHQ RAGQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVDEEIARMAGPQLVVP
Sbjct: 61 QARIDAWHQERAGQAHDAVAYKTFLQDIGYLLPEAADFQATTQNVDEEIARMAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN+IRG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGKGYNKIRGDKVIAFARAFLDEAA 180
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL GSHVDSTGY+I GKLVV+LK GS TGL+N AQL GFQG+A+AP A+LLKNNG+HF
Sbjct: 181 PLAAGSHVDSTGYKIVDGKLVVALKGGSNTGLRNDAQLIGFQGDAAAPTAILLKNNGLHF 240
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
EIQ+D ++P+GQTDAAGVKDILME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQVDASTPVGQTDAAGVKDILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
EE+ KGG+ TR MN DR YT DG+ EL+LHGRSLLF+RNVGHLMT DAILDK+GNEV
Sbjct: 301 SEEVAKGGQTFTRTMNADRTYTAIDGS-ELSLHGRSLLFVRNVGHLMTIDAILDKDGNEV 359
Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
PEGI+DGL T L ++HNLNGNTSRKNTRTGS+YIVKPKMHGPEE AF ELFGR+EDVLG
Sbjct: 360 PEGILDGLVTCLASMHNLNGNTSRKNTRTGSIYIVKPKMHGPEEAAFTNELFGRIEDVLG 419
Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
LPRNTLKVGIMDEERRTTINLKACIK A ERVVFINTGFLDRTGDEIHTSMEAGPMVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTINLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 479
Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
MKAEKWI AYEN+NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HPMAGANTAW
Sbjct: 480 DMKAEKWIGAYENSNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPMAGANTAW 539
Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
VPSPTAA LHA+HYHK+DV ARQ ELAKR AS+DDILTIPLA + W+ E+ +NELDNN
Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRAHASVDDILTIPLAVNPQWTAEQIKNELDNN 599
Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
SQGILGY+VRW++QGVGCSKVPDIND+ LMEDRATLRISSQH+ANW+RHG+VT++QV+ES
Sbjct: 600 SQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVTEEQVMES 659
Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
LKRMAPVVDRQN GD LYRP+AP+FD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNAGDALYRPLAPNFDSNIAFQAAVELVVEGTKQPNGYTEPVLHRRRREF 719
Query: 721 KAKNGL 726
KA NGL
Sbjct: 720 KAANGL 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: 1672
Number of extensions: 55
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 PfGW456L13_1139 (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.25976.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 1212.4 2.3 0 1212.2 2.3 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 Malate synthase G (EC 2.3.3.9)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 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 ! 1212.2 2.3 0 0 2 720 .. 4 722 .. 3 723 .. 0.99
Alignments for each domain:
== domain 1 score: 1212.2 bits; conditional E-value: 0
TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrd 56
+v++g+lqvak+l dfv++e++pgtg+ a+kfw+g d++++dlap+n+ llakrd
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 4 HVQVGGLQVAKVLFDFVNNEAIPGTGLTADKFWAGADKVIHDLAPKNKALLAKRD 58
6899*************************************************** PP
TIGR01345 57 eiqaaideyhrknk.gvidkeayksflkeigylveepervtietenvdseiasqa 110
++qa id++h++ + d ayk fl++igyl +e + +t+nvd+eia a
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 59 DFQARIDAWHQERAgQAHDAVAYKTFLQDIGYLLPEAADFQATTQNVDEEIARMA 113
************99557899*********************************** PP
TIGR01345 111 gpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkeynpkrgekv 165
gpqlvvpv+nar+alna+narwgslydalyg+++i+e dgaekgk yn rg+kv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 114 GPQLVVPVMNARFALNASNARWGSLYDALYGTDAISEADGAEKGKGYNKIRGDKV 168
******************************************************* PP
TIGR01345 166 iefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrg 220
i+far flde+ pl +gs+ d ykivd+kl+v l+ g+ t l++++q +g++g
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 169 IAFARAFLDEAAPLAAGSHVDSTGYKIVDGKLVVALKGGSNTGLRNDAQLIGFQG 223
******************************************************* PP
TIGR01345 221 daadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsva 275
daa+p++illk+nglh e+q+da p+g++d a+vkdi++e+a+tti+dcedsva
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 224 DAAAPTAILLKNNGLHFEIQVDASTPVGQTDAAGVKDILMEAALTTIMDCEDSVA 278
******************************************************* PP
TIGR01345 276 avdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangeelslhg 330
avda+dkv++yrn+lglmkg+l e++ k g++++r +n dr+yta +g+elslhg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 279 AVDADDKVVIYRNWLGLMKGDLSEEVAKGGQTFTRTMNADRTYTAIDGSELSLHG 333
******************************************************* PP
TIGR01345 331 rsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrk 385
rsllfvrnvghlmti +il+++g+e+pegildg++t++ ++++l+ + + +n+r+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 334 RSLLFVRNVGHLMTIDAILDKDGNEVPEGILDGLVTCLASMHNLNGNTSRKNTRT 388
******************************************************* PP
TIGR01345 386 gsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkac 440
gs+yivkpkmhgpee af+n+lf+ried+lgl+r+tlkvg+mdeerrt++nlkac
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 389 GSIYIVKPKMHGPEEAAFTNELFGRIEDVLGLPRNTLKVGIMDEERRTTINLKAC 443
******************************************************* PP
TIGR01345 441 iakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaag 495
i+ + erv+fintgfldrtgdeihtsmeag+mvrkadmk+ w+ aye++nv+ g
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 444 IKAASERVVFINTGFLDRTGDEIHTSMEAGPMVRKADMKAEKWIGAYENSNVDIG 498
******************************************************* PP
TIGR01345 496 ltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhy 550
l +gl+g+aqigkgmwampdlma mle+k+ + agantawvpsptaa+lhalhy
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 499 LSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPMAGANTAWVPSPTAAALHALHY 553
******************************************************* PP
TIGR01345 551 hrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyv 605
h+vdv++ q+ela+ +a+ ++iltip+a n +w++e+ik+eldnn qgilgyv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 554 HKVDVFARQAELAKR-AHASVDDILTIPLAVNPQWTAEQIKNELDNNSQGILGYV 607
*************99.8999*********************************** PP
TIGR01345 606 vrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvlesler 660
vrw++qg+gcskvpdi +v lmedratlrissqh+anwlrhgiv+ eqv+esl+r
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 608 VRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVTEEQVMESLKR 662
******************************************************* PP
TIGR01345 661 makvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrl 715
ma vvd+qnagd yrp+a+n+++ +af+aa +l+++gtkqp+gytep+lh+rr+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 663 MAPVVDRQNAGDALYRPLAPNFDSNIAFQAAVELVVEGTKQPNGYTEPVLHRRRR 717
******************************************************* PP
TIGR01345 716 efkek 720
efk+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1139 718 EFKAA 722
***86 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.75
//
[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