Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate H281DRAFT_03183 H281DRAFT_03183 glutamate dehydrogenase (NAD)
Query= uniprot:G8AE86 (1618 letters) >FitnessBrowser__Burk376:H281DRAFT_03183 Length = 1617 Score = 1577 bits (4083), Expect = 0.0 Identities = 855/1628 (52%), Positives = 1083/1628 (66%), Gaps = 27/1628 (1%) Query: 1 MALRAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAA 60 M + E+ L +VV R RL E F+R +YD V DD+ LYGAA Sbjct: 1 MQAKNEEAVTHLLNDVVEFARARLPEPTFHIVEPFLRHYYDFVDVDDLQSRSIPDLYGAA 60 Query: 61 LAMWQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGL 120 LA WQ Q R R ++RVYNP +E+HGW S TV+EIVNDDMPFLVDSV+ +NRQGL Sbjct: 61 LAHWQTAQ-RFVPGRERLRVYNPILEQHGWHSDHTVIEIVNDDMPFLVDSVSMAVNRQGL 119 Query: 121 TVHLVIHPVVRVKRDADGQLAELYEPA--AAPTDAAPESFMHVEVGAVTGAAALDQAREG 178 +H V+HPV R+ R DG +A + + + AA T + SF+H EV AA LD R+ Sbjct: 120 ALHSVVHPVFRIWRGPDGDIARVTQGSEEAADTRSQLASFIHFEVDRCGDAAKLDALRDD 179 Query: 179 LERVLADVRAAVADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHF 238 + +VL DVRAAV DW + + R I + A+ EA+AFL W DHF Sbjct: 180 IAKVLRDVRAAVEDWPKIVELARVTIKAMKVGESGPDAM-------EARAFLEWMVADHF 232 Query: 239 TFLGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLR---NYATLPPDVRDFL 295 TFLG+R+Y E G L V GSGLGI+RD+ + DG LPP + + Sbjct: 233 TFLGHRDY--ELVQQGTGYGLRAVPGSGLGIMRDE-LRATDGAAASPEVTVLPPAAAEII 289 Query: 296 RNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIP 355 + + +TK N + VHR +D IK A+G+++GER GL+TS AY S EIP Sbjct: 290 SSASPIFLTKANSRATVHRPGYLDYVGIKLAGADGKVVGERRFIGLYTSTAYFVSAAEIP 349 Query: 356 YLRRKVAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQR 415 +RRK A ++ AGF P+GH K+L+ +LETYPRDELFQ +L DIA+G+L LQE QR Sbjct: 350 IVRRKCANIVRRAGFLPKGHLAKSLVTVLETYPRDELFQADENQLYDIALGVLRLQEHQR 409 Query: 416 LALFVRKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARL 475 LFVR+D F+RF SCLV+VPRD+Y+T LR+RI ++L A++G FT L+ES LAR+ Sbjct: 410 TRLFVRRDRFDRFVSCLVFVPRDKYNTDLRQRIANLLTEAFNGASVEFTPLLSESTLARI 469 Query: 476 HFIIRTEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPT 535 HF++ +PG +P VD +LEARLVQ SR W D L DAL++A GEEQG L + YAD+FP Sbjct: 470 HFVVHAKPGGMPDVDTRELEARLVQVSRRWQDDLADALLDAFGEEQGNRLLQHYADSFPP 529 Query: 536 AYREEFNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLP 595 YR+++ A AV DIE IE+ L +NLYRP+EA K+Y G P+ LS LP Sbjct: 530 GYRDDYAARTAVRDIELIERVQGSERLAMNLYRPIEAGPRAFRFKVYRAGMPIALSRSLP 589 Query: 596 MLEHMDLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDG 655 MLEH+ ++V E P+ I G A P WIHDF + D VK+ F+DAF VW G Sbjct: 590 MLEHLGVRVDEERPYLIEALG-ATPAWIHDFGLEVVDDAEFDIERVKDLFEDAFEQVWTG 648 Query: 656 RMEDDGFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVAL 715 +E D FNRLVLRA L+AREVT+LRAYAKYLRQ + +E + G+PAIAR LV L Sbjct: 649 AIESDDFNRLVLRAQLSAREVTILRAYAKYLRQVGSTFSDAYIERAVTGNPAIARMLVEL 708 Query: 716 FHSRFDPA---RRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGA 772 F +RFDP+ R L I+ ALD V NLDEDRILR+FL ++ T RTN Y A Sbjct: 709 FIARFDPSLAGTRETRVENLLKTIDSALDQVPNLDEDRILRQFLGVIKATQRTNYYVFDA 768 Query: 773 DGRPKTYLSFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDF 832 DG+PK YLSFK + + LP P+PM E++VYSPR+EGVHLRGG+VARGG+RWSDRREDF Sbjct: 769 DGQPKPYLSFKFNPAQVPGLPEPKPMFEIWVYSPRVEGVHLRGGRVARGGLRWSDRREDF 828 Query: 833 RTEILGLMKAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDI 892 RTE+LGLMKAQMVKN VIVPVGSKGGFVVK PPP S R+A + EGI CY+T +RGLLD+ Sbjct: 829 RTEVLGLMKAQMVKNVVIVPVGSKGGFVVKNPPPQSE-RDAWMREGIACYQTFLRGLLDL 887 Query: 893 TDNLDAQGAVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGG 952 TDNL A VVPP +VVRHD DDPYLVVAADKGTATFSD AN++S ++GFWL DAFASGG Sbjct: 888 TDNL-AGTTVVPPRDVVRHDPDDPYLVVAADKGTATFSDYANAISQEYGFWLDDAFASGG 946 Query: 953 SAGYDHKKMGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIR 1012 S GYDHKKM ITARGAWESVKRHFRE+G DTQT DFTVVG+GDMSGDVFGNGMLLS HIR Sbjct: 947 SVGYDHKKMAITARGAWESVKRHFREMGVDTQTMDFTVVGIGDMSGDVFGNGMLLSPHIR 1006 Query: 1013 LLAAFDHRHIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLEL 1072 L+AAFDHRHIF+DP+PD A S ER RLF L RSSWADYD SL+SAGG VF R+AK++ L Sbjct: 1007 LVAAFDHRHIFLDPNPDPAASIAERGRLFLLDRSSWADYDPSLISAGGGVFPRTAKTIAL 1066 Query: 1073 TPEIRQRFGIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALR 1132 +P ++ GI+ ++P ELM+ +L+A VDLL+ GGIGTY+KA+ ET+ +VGD+ANDA+R Sbjct: 1067 SPAVQSVLGISAAALSPAELMRAILQAPVDLLYNGGIGTYVKASRETHLQVGDRANDAIR 1126 Query: 1133 IDGRDVRAKVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLND 1192 ++G D+R KV+ EG NLG+TQ GRIE AQ G R+NTDAIDNSAGVD SDHEVNIKILL Sbjct: 1127 VNGADLRCKVVAEGGNLGLTQLGRIEFAQRGGRINTDAIDNSAGVDCSDHEVNIKILLGL 1186 Query: 1193 VVVRGDMTLKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLE 1252 VV G+MT KQR+ LLA MTDEV LVL DNY Q+QAL++A G + L+A+ RL+R LE Sbjct: 1187 VVADGEMTAKQRNALLAEMTDEVGLLVLTDNYYQTQALSIAGRYGVELLDAETRLMRYLE 1246 Query: 1253 KAGRLNRAIEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMA 1312 +AGRLNRAIE+LP++EE++ R A ++GLT PE AVLLAY+K+ LYD LL S +P+DP ++ Sbjct: 1247 RAGRLNRAIEFLPNDEEVAERQAAKQGLTTPERAVLLAYSKMWLYDALLDSSVPEDPLVS 1306 Query: 1313 DDLTRYFPKPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADV 1372 D L YFP+PLR+ +E + RH LRREI+AT +TN+LVNR G FV +ME+T P D+ Sbjct: 1307 DMLIEYFPRPLRQRFSEPMQRHPLRREILATHLTNALVNRVGCEFVHRLMEETDAQPGDI 1366 Query: 1373 ARAYTIVRDAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQP--- 1429 RA + RD F L +W I+ LD V +Q M +E R +ER+A WFL P Sbjct: 1367 VRACIMARDVFDLDDVWRSIDALDNRVADDVQARMFVEVARLVERSALWFLRHLSSPGVN 1426 Query: 1430 -LDIARETEAFRPGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVL 1488 D+ R + L +L A + L+ R + GV +ELA R+A+ + Sbjct: 1427 SDDVTGLLARCRDAAQRLAPQWPALLPAADLEALSERQRVLVDAGVDSELAVRIASGEIS 1486 Query: 1489 AAAPDLVRIAGRTGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDD 1548 AA D+ +A R + VA VYF LG W+ ++AAA A++HW A A+ + + Sbjct: 1487 AALLDIAEVASTCKRKLELVAGVYFALGTLLNYNWISERAAALPAQSHWDMLARASALAE 1546 Query: 1549 LFAHQTALTTRVLEAVDQLPA-EAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAV 1607 L + ALT L + D +A V+AW R +ER +LL++LR LSML V Sbjct: 1547 LARLKRALTMSALASADDAATPDALVQAWRDKRATQLERYARLLADLRATGGASLSMLLV 1606 Query: 1608 ANRQLRGL 1615 R++ L Sbjct: 1607 IVREMAAL 1614 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: 5922 Number of extensions: 272 Number of successful extensions: 13 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: 1618 Length of database: 1617 Length adjustment: 51 Effective length of query: 1567 Effective length of database: 1566 Effective search space: 2453922 Effective search space used: 2453922 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