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)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752
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.7815.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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 7.33
//
[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:
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