Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate Ga0059261_1252 Ga0059261_1252 NAD-specific glutamate dehydrogenase
Query= uniprot:G8AE86 (1618 letters) >FitnessBrowser__Korea:Ga0059261_1252 Length = 1537 Score = 1015 bits (2624), Expect = 0.0 Identities = 625/1535 (40%), Positives = 849/1535 (55%), Gaps = 69/1535 (4%) Query: 89 GWQSHRTVVEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVVRVKRDADGQLAELYEPAA 148 G S + +VNDDMPFLVDS++A + + + VIHPVV V+R DG L + Sbjct: 61 GEDSRTMRLAVVNDDMPFLVDSISATIAAHDIAIRRVIHPVVAVERTGDGALTGI----- 115 Query: 149 APTDAAPESFMHVEVGAVTGAAALDQAREGLERVLADVRAAVADWRAMRQQVRAAIVEAD 208 + ES +++E+ R+ LER L VRAAV DW +R+ + D Sbjct: 116 -GAGGSRESMVYMELERADARDRTGLVRD-LERNLGHVRAAVTDWPELRRAM-----SDD 168 Query: 209 CARAAVPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLG 268 +R P E + L W T +G+ + + A +G+ Sbjct: 169 ASRVGDP---------EGASLLRWFQGGSMTLVGHEVWHIDGSVTDA---------AGIC 210 Query: 269 ILRDDSVTVFDGLRNYATLPPDVRDFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDA 328 ++ D+ + D R A V F + + ++ K N S VHR P+D L+ + Sbjct: 211 RMKLDTPLLADASRQLA-----VEWFEKGGQPPLLLKSNLISTVHRRAPLDLVLVPLREG 265 Query: 329 EGRIIGERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYP 388 G++ G + AGL+TS A + +P E+P LR ++ + GFDP+GH GKAL H L P Sbjct: 266 -GKVTGLSIHAGLWTSAALHSTPDEVPLLRARLTSLETKFGFDPRGHTGKALTHALTGLP 324 Query: 389 RDELFQIQVPELLDIAVGILHLQERQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRRI 448 D L IA+ + + +R R L + + R V++PRD T R I Sbjct: 325 HDLTIAFPQEALEQIALTAMSVTDRPRSKLVLIRSALGRHLFAFVWLPRDDVSTGRRVAI 384 Query: 449 QSILEAAYDGTCTGFTTQLTESVLARLHFIIRTE-PGRVPTVDATDLEARLVQASRGWDD 507 +LE + + T ++ L + +A L + + GR+P DA L+A L + RGW Sbjct: 385 GEMLERSANATQISWSIALEDGPVALLRYTLDLRGEGRMP--DAAALDAELERMVRGWLP 442 Query: 508 HLRDALVE-AHGEEQGRTLFRRYADAFPTAYREEFNAEAAVFDIERIEKATAQGTLGINL 566 + AL+E + + R+A AFP YR E A DI RI + Sbjct: 443 AVEAALIEDGLAANRAARMALRHAPAFPPGYRNHNGPEEAARDIVRIAGLADADARSVRF 502 Query: 567 YRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHMDLKVITEAPFEIAIAGHAAPVWIHDF 626 + + +L +K+Y G + LSD +P+ E+ +VI E P A++G +IHDF Sbjct: 503 FE----QAGKLRIKLYRLGGALALSDAVPVFENFGFRVIEELP--TALSGETG-AYIHDF 555 Query: 627 TAR--SQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAK 684 + L D V+E A AAV +GR E+D FNRL++ AG+ V +LRA+ + Sbjct: 556 EVELTGEAKLKGDIPTVEE----AIAAVLEGRAENDAFNRLIVEAGIAPASVVLLRAWFR 611 Query: 685 YLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRFDPARRSQNDPGLA---AEIERALD 741 YLRQ + YG V L PA+A LV F + DPAR + + A I LD Sbjct: 612 YLRQTGLTYGLVTVVEALRRAPAVATALVERFAAAHDPARAKGSAEAVKTADAAIAAGLD 671 Query: 742 GVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRNIDDLPLPRPMVEV 801 V +D+DRILR ++ TLRTNA+ A L+FK+DS + +LP P P E+ Sbjct: 672 AVSAIDDDRILRAIAGVIRATLRTNAFAPAA----AEALAFKLDSARVPNLPAPLPWREI 727 Query: 802 FVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNTVIVPVGSKGGFVV 861 +VYSPR+EG+HLR G VARGG+RWSDRR+DFRTEILGLMKAQ VKN VIVP G+KGGF Sbjct: 728 WVYSPRVEGIHLRAGPVARGGLRWSDRRDDFRTEILGLMKAQRVKNAVIVPTGAKGGFYP 787 Query: 862 KRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEVVRHDGDDPYLVVA 921 K+ P P+ R+A EG E Y+ +R LL ITDN+ G VV P V DG+DPY VVA Sbjct: 788 KQLPSPAIDRDAWFEEGKESYRIFIRSLLSITDNI-VSGKVVHPDSVAILDGEDPYFVVA 846 Query: 922 ADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGAWESVKRHFRELGH 981 ADKGTATFSD+AN+++++ FWLGDAFASGGS GYDHK MGITA+GAW SV+RHF E+G Sbjct: 847 ADKGTATFSDVANAIAIERNFWLGDAFASGGSVGYDHKAMGITAKGAWVSVQRHFLEMGT 906 Query: 982 DTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDPDAARSWEERQRLF 1041 D QTQ V G GDMSGDVFGNGMLLSK I+L+AAFDHRHIF+DPDPD A+SW+ER R+F Sbjct: 907 DVQTQSIRVAGCGDMSGDVFGNGMLLSKAIKLVAAFDHRHIFLDPDPDPAKSWDERARMF 966 Query: 1042 DLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVTPLELMQTLLKAEV 1101 L RSSWADYD SL+S GG VF R+ K ++L+P++R+ GI + + P L+ +LKA V Sbjct: 967 ALSRSSWADYDPSLISKGGGVFARTEKVIKLSPQVREVLGIDAEEMEPNALISAILKAPV 1026 Query: 1102 DLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGANLGVTQRGRIEAAQ 1161 DL+WFGGIGTY+KAA E + EVGD AND LR++ D+RA+ IGEGANLGVTQ RI + Sbjct: 1027 DLIWFGGIGTYVKAASEAHIEVGDPANDRLRVNAEDMRARAIGEGANLGVTQAARIAFSL 1086 Query: 1162 HGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQRDQLLAAMTDEVAGLVLA 1221 G RLNTD IDNSAGVD SD+EVNIKI LN V+ G + + R+ LLA+MTD+VA LVL Sbjct: 1087 RGGRLNTDFIDNSAGVDCSDNEVNIKIALNREVIEGRLKIDDRNTLLASMTDDVAHLVLE 1146 Query: 1222 DNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEYLPDEEELSARMANREGLT 1281 DN LQ+ AL+ G A+ + R+I LE +GRL+RA+E L E+ R GLT Sbjct: 1147 DNRLQTLALSFLENDGAVAVPSFVRVIEILEASGRLDRAVEGLGSNEDYLRRAQEGRGLT 1206 Query: 1282 RPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFPKPLRKAHAEAVGRHRLRREII 1341 RPELAVLLA +K+ L D + DL DP + DL FP ++K + + HRLR EI+ Sbjct: 1207 RPELAVLLATSKLALQDAIEDGDLGLDPELEPDLIAAFPPAMQKKFKKPIEEHRLRGEIV 1266 Query: 1342 ATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAFGLRSLWTGIEDLDTVVPA 1401 AT + N +VNR G E+ E+ G D+A + + FGL ++W IE A Sbjct: 1267 ATKLANRIVNRLGVLHPFELAEEEGASLRDIAAMFVVAERLFGLPAIWEAIETAAISEQA 1326 Query: 1402 ALQTSMILETVRHMERAAAWFLASCQQPLDIARETEA-FRPGIETLLAGLDNVLDAEETA 1460 L +L+ V RA L +P + E A +PGI L +L E A Sbjct: 1327 RL---ALLDEVAVATRAQIADLLRVDRPDEGPGELIARLKPGIAGLDRQTKKLLKEEARA 1383 Query: 1461 RLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGRGVADVAAVYFMLGRRFG 1520 + A +E G P +L ++ + L A L + R G ++ + LG+ G Sbjct: 1384 QSGRIAAKLEEAGAPHDLVTKIVRIFELDGAVGLADLGQRRGIDETELTHAFTHLGQELG 1443 Query: 1521 LEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRVLEAVDQLPAEAPVEAWIAHR 1580 L+W + AA A + W++ +A L D L L D A V+AW+A Sbjct: 1444 LDWAQAVAARIVAGDPWERLLIAGLARDF----QQLRLEFLARADGKDPRAAVDAWLADH 1499 Query: 1581 RPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGL 1615 VE+ L++ R P + +MLA Q R L Sbjct: 1500 GARVEQFAALVARARKAPTPNAAMLAQIAGQARVL 1534 Lambda K H 0.320 0.136 0.399 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: 5596 Number of extensions: 270 Number of successful extensions: 14 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 1618 Length of database: 1537 Length adjustment: 51 Effective length of query: 1567 Effective length of database: 1486 Effective search space: 2328562 Effective search space used: 2328562 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 61 (28.1 bits)
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