Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Pf6N2E2_4752 Malate synthase G (EC 2.3.3.9)
Query= reanno::psRCH2:GFF353
(726 letters)
>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 Malate synthase G (EC
2.3.3.9)
Length = 725
Score = 1230 bits (3183), Expect = 0.0
Identities = 596/726 (82%), Positives = 665/726 (91%), Gaps = 1/726 (0%)
Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
MTE VQVGGLQVAKVL+DFVNNEAIPGTG+ A AFWAGAD VIHDLAPKN+ALLAKRDD
Sbjct: 1 MTEHVQVGGLQVAKVLFDFVNNEAIPGTGLTADAFWAGADKVIHDLAPKNKALLAKRDDF 60
Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
QA+IDAWHQAR GQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61 QARIDAWHQARTGQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120
Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
+MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN++RG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAA 180
Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
PL GSHVDS Y+I GKLVV+LK GS +GL++ AQL GFQG+ASAP VLLK+NG+HF
Sbjct: 181 PLAAGSHVDSIAYKIVDGKLVVTLKGGSNSGLRDDAQLIGFQGDASAPTTVLLKHNGLHF 240
Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
EIQID ++P+GQTDAAGVKDILME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGVKDILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300
Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
EE+ KGG+ TR MNPDRVYT DG+ +TLHGRSLLF+RNVGHLMT DAILD+ GNEV
Sbjct: 301 AEEVAKGGQTFTRTMNPDRVYTAVDGSS-VTLHGRSLLFVRNVGHLMTIDAILDQHGNEV 359
Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
PEGI+DGL TSL A+H+LNGNTSR+N+RTGS+YIVKPKMHGPEE AF ELFGRVEDVL
Sbjct: 360 PEGILDGLITSLAAIHSLNGNTSRRNSRTGSVYIVKPKMHGPEEAAFTNELFGRVEDVLN 419
Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAGPMVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 479
Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
MKAEKWI AYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 DMKAEKWIGAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539
Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
VPSPTAA LHA+HYHK+DV ARQ ELAKR +AS+DDILTIPLA + NW+ E+ +NELDNN
Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRARASVDDILTIPLAVNPNWTPEQIKNELDNN 599
Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
+QGILGY+VRW++QGVGCSKVPDINDI LMEDRATLRISSQH+ANW+RHG+VT+DQV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHIANWLRHGIVTQDQVMES 659
Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
LKRMAPVVDRQN DPLYRP+APDFD ++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNASDPLYRPLAPDFDRNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 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: 1643
Number of extensions: 52
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 Pf6N2E2_4752 (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.20253.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 1209.6 1.2 0 1209.4 1.2 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 Malate synthase G (EC 2.3.3.9)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 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 ! 1209.4 1.2 0 0 2 720 .. 4 722 .. 3 723 .. 0.99
Alignments for each domain:
== domain 1 score: 1209.4 bits; conditional E-value: 0
TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaidey 65
+v++g+lqvak+l dfv++e++pgtg+ a++fw+g d++++dlap+n+ llakrd++qa id++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 4 HVQVGGLQVAKVLFDFVNNEAIPGTGLTADAFWAGADKVIHDLAPKNKALLAKRDDFQARIDAW 67
6899************************************************************ PP
TIGR01345 66 hrknk.gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaa 128
h+ + + d ayk fl++igyl +e + +t+nvd+eia agpqlvvpv+nar+alna+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 68 HQARTgQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNAS 131
***99557899***************************************************** PP
TIGR01345 129 narwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkyki 192
narwgslydalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d ++yki
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 132 NARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSIAYKI 195
**************************************************************** PP
TIGR01345 193 vdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvk 256
vd+kl+v+l+ g+ l+d++q +g++gda++p+++llk+nglh e+qida p+g++d a+vk
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 196 VDGKLVVTLKGGSNSGLRDDAQLIGFQGDASAPTTVLLKHNGLHFEIQIDASTPVGQTDAAGVK 259
**************************************************************** PP
TIGR01345 257 divlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsyta 320
di++e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n dr+yta
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 260 DILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLAEEVAKGGQTFTRTMNPDRVYTA 323
**************************************************************** PP
TIGR01345 321 angeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsr 384
+g+ ++lhgrsllfvrnvghlmti +il+++g+e+pegildg++ts+ a++ l+ + + rnsr
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 324 VDGSSVTLHGRSLLFVRNVGHLMTIDAILDQHGNEVPEGILDGLITSLAAIHSLNGNTSRRNSR 387
**************************************************************** PP
TIGR01345 385 kgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkerv 448
+gsvyivkpkmhgpee af+n+lf+r+ed+l+l+r+tlkvg+mdeerrt++nlkaci+ + erv
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 388 TGSVYIVKPKMHGPEEAAFTNELFGRVEDVLNLPRNTLKVGIMDEERRTTVNLKACIKAASERV 451
**************************************************************** PP
TIGR01345 449 afintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwa 512
+fintgfldrtgdeihtsmeag+mvrkadmk+ w+ aye+ nv+ gl +gl+g+aqigkgmwa
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 452 VFINTGFLDRTGDEIHTSMEAGPMVRKADMKAEKWIGAYENWNVDIGLSTGLQGRAQIGKGMWA 515
**************************************************************** PP
TIGR01345 513 mpdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeilt 576
mpdlma mle+k+ + agantawvpsptaa+lhalhyh+vdv++ q+ela+ ra+ ++ilt
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 516 MPDLMAAMLEQKIAHPLAGANTAWVPSPTAAALHALHYHKVDVFARQAELAKR-ARASVDDILT 578
***************************************************99.899******* PP
TIGR01345 577 ipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhl 640
ip+a n nw+ e+ik+eldnn+qgilgyvvrw++qg+gcskvpdi ++ lmedratlrissqh+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 579 IPLAVNPNWTPEQIKNELDNNAQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHI 642
**************************************************************** PP
TIGR01345 641 anwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsg 704
anwlrhgiv+++qv+esl+rma vvd+qna d+ yrp+a+++++ +af+aa +l+++gtkqp+g
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 643 ANWLRHGIVTQDQVMESLKRMAPVVDRQNASDPLYRPLAPDFDRNIAFQAAVELVIEGTKQPNG 706
**************************************************************** PP
TIGR01345 705 ytepilharrlefkek 720
ytep+lh+rr+efk+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 707 YTEPVLHRRRREFKAA 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.33
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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