Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate Pf1N1B4_4643 NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form
Query= SwissProt::Q9HZE0 (1620 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4643 Length = 1635 Score = 2704 bits (7009), Expect = 0.0 Identities = 1337/1616 (82%), Positives = 1467/1616 (90%), Gaps = 2/1616 (0%) Query: 1 MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60 MAFFTAASKADFQHQLQ ALAQH+ ++ALPQV LFAEQFF +ISLDELTQRRLSDL GCT Sbjct: 1 MAFFTAASKADFQHQLQAALAQHISEQALPQVALFAEQFFGIISLDELTQRRLSDLAGCT 60 Query: 61 LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120 LSAWRLLERFD P+VRVYNPDYE+HGWQSTHTAVEVLH DLPFLVDSVR ELNRRGYS Sbjct: 61 LSAWRLLERFDHAHPQVRVYNPDYERHGWQSTHTAVEVLHHDLPFLVDSVRTELNRRGYS 120 Query: 121 IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180 IHTLQT VLSVRR +KGEL EILPKG+QG+ + QESLMYLEIDRCA+ EL L K + + Sbjct: 121 IHTLQTTVLSVRRGSKGELLEILPKGTQGEGILQESLMYLEIDRCANTAELNVLTKELEQ 180 Query: 181 VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240 VLGEVRV VADFEPMKAK +EL+ + ++ + A+E E++S+LEWL+ NHFTFLGYEE Sbjct: 181 VLGEVRVAVADFEPMKAKVQELIEGIDNSQFIINADEKSEIKSFLEWLVGNHFTFLGYEE 240 Query: 241 FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAYLREPVLLSFAKAAHPS 300 F V ++ +GG + YD+ SFLGLT+LLRAGL+ DDL IEDYAV YLREP LSFAKAAHPS Sbjct: 241 FVVGEDQNGGHIEYDQNSFLGLTKLLRAGLTVDDLRIEDYAVNYLREPTPLSFAKAAHPS 300 Query: 301 RVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGF 360 RVHRPAYPDYVSIR++D G+V++ECRFMGL+TSSVY ESV IP+IR KV + +RSGF Sbjct: 301 RVHRPAYPDYVSIRQIDANGKVVKECRFMGLYTSSVYGESVRVIPYIRRKVEIIEQRSGF 360 Query: 361 DTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRFCY 420 KAHLGKELAQVLEVLPRDDLFQTPVDELF+T ++IV+IQERNKIRVFLRKDPYGRFCY Sbjct: 361 QAKAHLGKELAQVLEVLPRDDLFQTPVDELFTTVMSIVQIQERNKIRVFLRKDPYGRFCY 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+QACRSWQDDY+SLVVE+ GEA+GTNVLADFPKGFPAGYRERFA H AVVD+ Sbjct: 481 PVLLEKEVVQACRSWQDDYASLVVESFGEAQGTNVLADFPKGFPAGYRERFAAHSAVVDM 540 Query: 541 QHLLSLSEQRPLVMSFYQPLAQ--GEQQLHCKLYHADTPLALSDVLPILENLGLRVLGEF 598 QHLLSLSE+ PLVMSFYQPLAQ G++ LHCKLYHADTPLALSDVLPILENLGLRVLGEF Sbjct: 541 QHLLSLSEKNPLVMSFYQPLAQVSGQRMLHCKLYHADTPLALSDVLPILENLGLRVLGEF 600 Query: 599 PYRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTA 658 PYRLRH +GRE+WIHDFAFT AEGL++DIQQLN+ LQDAFVHIV GDAENDAFNRLVLTA Sbjct: 601 PYRLRHNSGREFWIHDFAFTAAEGLELDIQQLNDTLQDAFVHIVRGDAENDAFNRLVLTA 660 Query: 659 NLPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAE 718 LPWRDVALLRAYARY+KQIRLGFDLGYIAS LN HTDIAREL RLFKTRFYLARKL ++ Sbjct: 661 GLPWRDVALLRAYARYMKQIRLGFDLGYIASTLNNHTDIARELTRLFKTRFYLARKLASD 720 Query: 719 DLEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFK 778 DLEDKQQ+LE AIL ALD+VQVLNEDRILRRYLDLIKATLRTNFYQ D +GQNKSYFSFK Sbjct: 721 DLEDKQQRLEHAILAALDDVQVLNEDRILRRYLDLIKATLRTNFYQTDTHGQNKSYFSFK 780 Query: 779 FNPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQ 838 FNP IPELP+PVPK+EIFVYSPRVEGVHLR G VARGGLRWSDREEDFRTEVLGLVKAQ Sbjct: 781 FNPHQIPELPKPVPKFEIFVYSPRVEGVHLRFGNVARGGLRWSDREEDFRTEVLGLVKAQ 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+SF ERQRLF+LPRS+W+DYD ++S GGGIF RSAKSIAI+P+MK RFDIQAD Sbjct: 1021 PNPEPANSFAERQRLFDLPRSAWSDYDTSIMSEGGGIFSRSAKSIAISPQMKERFDIQAD 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 +NTDFIDNAGGVDCSDHEVNIKILLNEVV AGDMT+KQRN Sbjct: 1141 GGNLGMTQLGRVEFGLNGGGSNTDFIDNAGGVDCSDHEVNIKILLNEVVHAGDMTDKQRN 1200 Query: 1199 ALLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLP 1258 LL MTD VG LVLGNNYKQTQALSLA RRA RIAEYKRLM DLE RGKLDRA+EFLP Sbjct: 1201 QLLASMTDEVGNLVLGNNYKQTQALSLAARRAFVRIAEYKRLMNDLEGRGKLDRAIEFLP 1260 Query: 1259 SDEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAE 1318 ++E + ER++ G GLTRAELSVLISYSKIDLKE+LL SLVPDDDYLTRDMETAFP L Sbjct: 1261 AEEAINERLAEGHGLTRAELSVLISYSKIDLKEALLNSLVPDDDYLTRDMETAFPPTLVS 1320 Query: 1319 KFGDAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHL 1378 KF AMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMS ANVAGAYVIVRD+FHL Sbjct: 1321 KFSAAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSPANVAGAYVIVRDIFHL 1380 Query: 1379 PHWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAA 1438 PHWFRQIE LDYQV AD+QL LMDELMRLGRRATRWFLRSRRNE +AARDVAHFGP +AA Sbjct: 1381 PHWFRQIEALDYQVSADVQLELMDELMRLGRRATRWFLRSRRNEQNAARDVAHFGPHLAA 1440 Query: 1439 LGLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDT 1498 LGLKL+ELLEGPTRE WQ RYQ YV AGVPELLARMVAGT+HLYTLLPIIEASDVTGQ+ Sbjct: 1441 LGLKLDELLEGPTREGWQTRYQAYVAAGVPELLARMVAGTTHLYTLLPIIEASDVTGQNA 1500 Query: 1499 AEVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQD 1558 A+VAKAYFAVGSALD+TWYLQQI+ LPVENNWQALAREAFRDD+DWQQRAIT+SVLQ D Sbjct: 1501 ADVAKAYFAVGSALDITWYLQQISALPVENNWQALAREAFRDDVDWQQRAITISVLQQGD 1560 Query: 1559 GPKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQ 1614 G ++VE R+ LW+E+H ++ERWRAMLVE+RAASGTDYAMYAVANREL+DLA S Q Sbjct: 1561 GTQDVETRLALWMEEHEGMIERWRAMLVEIRAASGTDYAMYAVANRELLDLALSGQ 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: 6612 Number of extensions: 244 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: 1635 Length adjustment: 52 Effective length of query: 1568 Effective length of database: 1583 Effective search space: 2482144 Effective search space used: 2482144 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