Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate GFF2946 PS417_15075 NAD-glutamate dehydrogenase
Query= SwissProt::Q9HZE0 (1620 letters) >FitnessBrowser__WCS417:GFF2946 Length = 1622 Score = 2712 bits (7031), Expect = 0.0 Identities = 1343/1616 (83%), Positives = 1466/1616 (90%), Gaps = 2/1616 (0%) Query: 1 MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60 MAFFTAASKADFQHQLQ ALAQH+ ++ALPQV LFAEQFF +ISLDELTQRRLSDL GCT Sbjct: 1 MAFFTAASKADFQHQLQAALAQHISEQALPQVALFAEQFFGIISLDELTQRRLSDLAGCT 60 Query: 61 LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120 LSAWRLLERFD QP+VRVYNPDYE+HGWQSTHTAVEVLH DLPFLVDSVR ELNRRGYS Sbjct: 61 LSAWRLLERFDHTQPQVRVYNPDYERHGWQSTHTAVEVLHHDLPFLVDSVRTELNRRGYS 120 Query: 121 IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180 IHTLQT VLSVRR AKGEL EILPKG+QG+ + QESLMYLEIDRCA+A EL L K + + Sbjct: 121 IHTLQTTVLSVRRGAKGELLEILPKGTQGEGIQQESLMYLEIDRCANAAELNVLSKELEQ 180 Query: 181 VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240 VLGEVRV VADFEPMKAK ++LL + ++ + EE E++++LEWL+ NHFTFLGYEE Sbjct: 181 VLGEVRVAVADFEPMKAKVQDLLAGIDASQFSIDGEEKAEIKNFLEWLVGNHFTFLGYEE 240 Query: 241 FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAYLREPVLLSFAKAAHPS 300 F V DEADGG + YD SFLGLT+LLRAGL+ DDL IEDYAVAYLREP +LSFAKAAHPS Sbjct: 241 FVVRDEADGGHIEYDADSFLGLTKLLRAGLTADDLRIEDYAVAYLREPTVLSFAKAAHPS 300 Query: 301 RVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGF 360 RVHRPAYPDYVSIRE+ G+VI+E RFMGL+TSSVY ESV IP+IR KVAE+ RRSGF Sbjct: 301 RVHRPAYPDYVSIREISADGKVIKEHRFMGLYTSSVYGESVRVIPYIRRKVAEIERRSGF 360 Query: 361 DTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRFCY 420 KAHLGKELAQV+EVLPRDDLFQTPVDELFST ++IV+IQERNKIRVFLRKDPYGRFCY Sbjct: 361 QPKAHLGKELAQVVEVLPRDDLFQTPVDELFSTVMSIVQIQERNKIRVFLRKDPYGRFCY 420 Query: 421 CLAYVPRDVYSTETRLKIQQVLMERLQASDCEFWTFFSESVLARVQFILRVDPKSRIDID 480 CLAYVPRD+YSTE R KIQQVLM+RL+ASDCEFWTFFSESVLARVQ ILRVDPK+R+DID Sbjct: 421 CLAYVPRDIYSTEVRQKIQQVLMDRLKASDCEFWTFFSESVLARVQLILRVDPKNRLDID 480 Query: 481 PARLEEEVIQACRSWQDDYSSLVVENLGEAKGTNVLADFPKGFPAGYRERFAPHFAVVDL 540 P +LE+EV+QACRSWQDDYSSLVVE+ GEA GTNVLADFPKGFPAGYRERFA H AVVD+ Sbjct: 481 PLQLEKEVVQACRSWQDDYSSLVVESFGEAHGTNVLADFPKGFPAGYRERFAAHSAVVDM 540 Query: 541 QHLLSLSEQRPLVMSFYQPLAQ--GEQQLHCKLYHADTPLALSDVLPILENLGLRVLGEF 598 QHLLSL+E PLVMSFYQPL Q G+++LHCKLYHADTPLALSDVLPILENLGLRVLGEF Sbjct: 541 QHLLSLTEANPLVMSFYQPLGQVSGQRELHCKLYHADTPLALSDVLPILENLGLRVLGEF 600 Query: 599 PYRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTA 658 PYRLRH NGRE+WIHDFAF AEG+++DIQQLN+ LQDAFVHIV GDAENDAFNRLVLTA Sbjct: 601 PYRLRHANGREFWIHDFAFIAAEGVNLDIQQLNDTLQDAFVHIVHGDAENDAFNRLVLTA 660 Query: 659 NLPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAE 718 LPWRDVALLRAYARYLKQIRLGFDLGYIAS LN HTDIAREL RLFKTRFYLARKLTA+ Sbjct: 661 GLPWRDVALLRAYARYLKQIRLGFDLGYIASTLNNHTDIARELTRLFKTRFYLARKLTAD 720 Query: 719 DLEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFK 778 DLEDKQQ+LEQAIL ALD+VQVLNEDRILRRYLDLIKATLRTNFYQ D NGQNKSYFSFK Sbjct: 721 DLEDKQQRLEQAILSALDDVQVLNEDRILRRYLDLIKATLRTNFYQTDANGQNKSYFSFK 780 Query: 779 FNPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQ 838 F+P+AIPELP+PVPK+EIFVYSPRVEGVHLR G VARGGLRWSDREEDFRTEVLGLVKAQ Sbjct: 781 FDPRAIPELPKPVPKFEIFVYSPRVEGVHLRFGNVARGGLRWSDREEDFRTEVLGLVKAQ 840 Query: 839 QVKNAVIVPVGAKGGFVPRRLPLGGSRDEIQAEAIACYRIFISGLLDITDNLKEGEVVPP 898 QVKN+VIVPVGAKGGF+PRRLPLGGSRDEI AE IACYRIFISGLLDITDNLK+G +VPP Sbjct: 841 QVKNSVIVPVGAKGGFLPRRLPLGGSRDEIAAEGIACYRIFISGLLDITDNLKDGALVPP 900 Query: 899 ANVVRHDEDDPYLVVAADKGTATFSDIANGIAAEYGFWLGDAFASGGSAGYDHKGMGITA 958 ANVVRHD+DDPYLVVAADKGTATFSDIANGIA +YGFWLGDAFASGGSAGYDHK MGITA Sbjct: 901 ANVVRHDDDDPYLVVAADKGTATFSDIANGIAIDYGFWLGDAFASGGSAGYDHKKMGITA 960 Query: 959 KGAWVSVQRHFRERGIDVQKDNISVIGIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFID 1018 KGAWV VQRHFRERGI+VQ+D+I+V+G+GDMAGDVFGNGLLMSDKLQLVAAFNH+HIFID Sbjct: 961 KGAWVGVQRHFRERGINVQEDSITVVGVGDMAGDVFGNGLLMSDKLQLVAAFNHLHIFID 1020 Query: 1019 PNPDAASSFVERQRLFNLPRSSWADYDAKLISAGGGIFLRSAKSIAITPEMKARFDIQAD 1078 PNP+ A+SFVERQR+F LPRS+W DYD ++S GGGIF RSAKSIAI+P+MK RFDI AD Sbjct: 1021 PNPNPATSFVERQRMFELPRSAWTDYDTSIMSEGGGIFSRSAKSIAISPQMKERFDISAD 1080 Query: 1079 RLAPTELIHALLKAPVDLLWNGGIGTYVKSSKETHADVGDKANDGLRVDGRELRAKVVGE 1138 +L PTEL++ALLKAPVDLLWNGGIGTYVK+S E+HADVGDKAND LRV+G ELR KVVGE Sbjct: 1081 KLTPTELLNALLKAPVDLLWNGGIGTYVKASTESHADVGDKANDALRVNGNELRCKVVGE 1140 Query: 1139 GGNLGMTQLARVEFGLHGGANNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRN 1198 GGNLGMTQL RVEFGL+GG +NTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMT+KQRN Sbjct: 1141 GGNLGMTQLGRVEFGLNGGGSNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTDKQRN 1200 Query: 1199 ALLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLP 1258 LL MTD VG LVLGNNYKQTQALSLA RRA ER AEYKRLM DLE RGKLDRA+E+LP Sbjct: 1201 QLLASMTDEVGNLVLGNNYKQTQALSLAARRAYERAAEYKRLMSDLEGRGKLDRAIEYLP 1260 Query: 1259 SDEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAE 1318 ++E+L ER + G+GLTR ELSVLISYSKIDLKE+LLKSLVPDD+YLTRDMETAFP L Sbjct: 1261 TEEQLTERAATGKGLTRPELSVLISYSKIDLKEALLKSLVPDDEYLTRDMETAFPPSLVA 1320 Query: 1319 KFGDAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHL 1378 KF +AMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMS ANVAGAYVIVRD+FHL Sbjct: 1321 KFSEAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSPANVAGAYVIVRDIFHL 1380 Query: 1379 PHWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAA 1438 PHWFRQIE LD+QV AD+QL LMDELMRLGRRATRWFLRSRRNE DA RD AHFGP +AA Sbjct: 1381 PHWFRQIEALDHQVSADVQLELMDELMRLGRRATRWFLRSRRNEQDAGRDTAHFGPHLAA 1440 Query: 1439 LGLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDT 1498 LGLKL+ELLEGPTRE WQ RY Y +AGVPELLARMVAGT+HLYTLLPIIEA+DVTG D Sbjct: 1441 LGLKLDELLEGPTREGWQNRYGKYTEAGVPELLARMVAGTTHLYTLLPIIEAADVTGHDA 1500 Query: 1499 AEVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQD 1558 AEVAKAYFAVGSALDL WYLQQI++LPV NNWQA AREAFRDD+DWQQRAIT+SVLQM D Sbjct: 1501 AEVAKAYFAVGSALDLPWYLQQISDLPVANNWQAQAREAFRDDVDWQQRAITISVLQMAD 1560 Query: 1559 GPKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQ 1614 P+++EARV LWLEQH + +RW AM+VE+RAA GTDYAMYAVANREL+DLA S Q Sbjct: 1561 APQDMEARVALWLEQHKDMADRWVAMMVEIRAAVGTDYAMYAVANRELLDLALSGQ 1616 Lambda K H 0.321 0.137 0.403 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: 6529 Number of extensions: 251 Number of successful extensions: 3 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: 1620 Length of database: 1622 Length adjustment: 51 Effective length of query: 1569 Effective length of database: 1571 Effective search space: 2464899 Effective search space used: 2464899 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 (21.9 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