Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate AO353_07560 AO353_07560 malate synthase G
Query= reanno::psRCH2:GFF353 (726 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07560 Length = 725 Score = 1221 bits (3159), Expect = 0.0 Identities = 591/726 (81%), Positives = 666/726 (91%), Gaps = 1/726 (0%) Query: 1 MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60 MTE VQVGGLQVAKVL+DFVNNEAIPG+G+ A FWAGAD VIHDLAPKN+ALLAKRDDL Sbjct: 1 MTEHVQVGGLQVAKVLFDFVNNEAIPGSGLTADKFWAGADKVIHDLAPKNKALLAKRDDL 60 Query: 61 QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120 QA+IDAWHQ+RAGQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP Sbjct: 61 QARIDAWHQSRAGQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120 Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180 +MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN++RG+KVIA+AR FL+EAA Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAA 180 Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240 PL GSHVDSTGY+I KLVVSLK GS +GL+N AQL GF G+A+AP A+LLKNNG+HF Sbjct: 181 PLAAGSHVDSTGYKIVDRKLVVSLKGGSNSGLRNDAQLIGFHGDAAAPTAILLKNNGLHF 240 Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300 EIQID ++P+GQTDAAGVKD+LME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL Sbjct: 241 EIQIDASTPVGQTDAAGVKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300 Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360 EE+ KGGK TR MN DR YT DG+ EL+LHGRSLLF+RNVGHLMT DAILDK GNEV Sbjct: 301 SEEVAKGGKTFTRTMNADRTYTAPDGS-ELSLHGRSLLFVRNVGHLMTIDAILDKNGNEV 359 Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420 PEGI+DGL T+L A+H+LNGNT+RKN+RTGS+YIVKPKMHGPEE AF ELFGR+EDVL Sbjct: 360 PEGILDGLVTNLAALHSLNGNTTRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIEDVLE 419 Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480 LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAG MVRKA Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGAMVRKA 479 Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540 MKAEKWISAYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW Sbjct: 480 DMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539 Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600 VPSPTAA LHA+HYHK+DV ARQ ELAKR +AS+DDILTIPLA D NW+ E+ +NELDNN Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRARASLDDILTIPLASDPNWTAEQIQNELDNN 599 Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660 +QGILGY+VRW++QGVGCSKVPDIND+ LMEDRATLRISSQH+ANW+RHG+V++ QV+E+ Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVSEAQVLET 659 Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720 LKRMAPVVDRQN DPLYRP+AP+FD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF Sbjct: 660 LKRMAPVVDRQNANDPLYRPLAPNFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 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: 1627 Number of extensions: 51 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 AO353_07560 AO353_07560 (malate synthase G)
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.11436.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 1217.2 1.6 0 1217.0 1.6 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 AO353_07560 malate synthase G Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 AO353_07560 malate synthase G # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1217.0 1.6 0 0 2 720 .. 4 722 .. 3 723 .. 0.99 Alignments for each domain: == domain 1 score: 1217.0 bits; conditional E-value: 0 TIGR01345 2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyh 66 +v++g+lqvak+l dfv++e++pg g+ a+kfw+g d++++dlap+n+ llakrd++qa id++h lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 4 HVQVGGLQVAKVLFDFVNNEAIPGSGLTADKFWAGADKVIHDLAPKNKALLAKRDDLQARIDAWH 68 6899************************************************************* PP TIGR01345 67 rknk.gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaana 130 ++ + d ayk fl++igyl +e + +t+nvd+eia agpqlvvpv+nar+alna+na lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 69 QSRAgQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNASNA 133 **99557899******************************************************* PP TIGR01345 131 rwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdk 195 rwgslydalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d ykivd+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 134 RWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSTGYKIVDR 198 ***************************************************************** PP TIGR01345 196 klavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivl 260 kl+v l+ g+ l++++q +g++gdaa+p++illk+nglh e+qida p+g++d a+vkd+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 199 KLVVSLKGGSNSGLRNDAQLIGFHGDAAAPTAILLKNNGLHFEIQIDASTPVGQTDAAGVKDVLM 263 ***************************************************************** PP TIGR01345 261 esaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangee 325 e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n dr+yta++g+e lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 264 EAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLSEEVAKGGKTFTRTMNADRTYTAPDGSE 328 ***************************************************************** PP TIGR01345 326 lslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyi 390 lslhgrsllfvrnvghlmti +il+++g+e+pegildg++t++ al+ l+ + + +nsr+gsvyi lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 329 LSLHGRSLLFVRNVGHLMTIDAILDKNGNEVPEGILDGLVTNLAALHSLNGNTTRKNSRTGSVYI 393 ***************************************************************** PP TIGR01345 391 vkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgf 455 vkpkmhgpee af+n+lf+ried+l+l+r+tlkvg+mdeerrt++nlkaci+ + erv+fintgf lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 394 VKPKMHGPEEAAFTNELFGRIEDVLELPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGF 458 ***************************************************************** PP TIGR01345 456 ldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaem 520 ldrtgdeihtsmeagamvrkadmk+ w++aye+ nv+ gl +gl+g+aqigkgmwampdlma m lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 459 LDRTGDEIHTSMEAGAMVRKADMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAM 523 ***************************************************************** PP TIGR01345 521 lekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnw 585 le+k+ + agantawvpsptaa+lhalhyh+vdv++ q+ela+ ra+l++iltip+a++ nw lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 524 LEQKIAHPLAGANTAWVPSPTAAALHALHYHKVDVFARQAELAKR-ARASLDDILTIPLASDPNW 587 *******************************************99.899**************** PP TIGR01345 586 seeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivs 650 ++e+i++eldnn+qgilgyvvrw++qg+gcskvpdi +v lmedratlrissqh+anwlrhgivs lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 588 TAEQIQNELDNNAQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVS 652 ***************************************************************** PP TIGR01345 651 keqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrl 715 qvle+l+rma vvd+qna d+ yrp+a+n+++ +af+aa +l+++gtkqp+gytep+lh+rr+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 653 EAQVLETLKRMAPVVDRQNANDPLYRPLAPNFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRR 717 ***************************************************************** PP TIGR01345 716 efkek 720 efk+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06 # Mc/sec: 8.19 // [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