Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate 5209331 Shew_1809 NAD-glutamate dehydrogenase (RefSeq)
Query= SwissProt::E1V4J5 (1613 letters) >FitnessBrowser__PV4:5209331 Length = 1614 Score = 1449 bits (3750), Expect = 0.0 Identities = 754/1600 (47%), Positives = 1067/1600 (66%), Gaps = 16/1600 (1%) Query: 13 LLKQLKERLQSRLDKDKAAEVDTFAHLFYAAVPLEDLADRRLDDLYGATLSVWHFIQQFD 72 LL+ + + S++ +A +V+ FA YA + +DL R DLYGA LS+W+ + Sbjct: 11 LLENVVSLIHSKVPNTQAKQVEQFATCIYAHMSKDDLQHRNDSDLYGAVLSLWNAANKTP 70 Query: 73 PEAPKVRVLNPDFEEHGWQSTHTFIAVLHEDMPFLVDSVRVELNRRGMTVHAIHNAVLAV 132 +RV NP +HGW+S+H+ I V+ DMPFLVDSV + LNR G+T H + + L V Sbjct: 71 VGETHIRVFNPSQSKHGWKSSHSIIEVIQPDMPFLVDSVGMALNRMGITTHMMLHTPLTV 130 Query: 133 GRDDEHRLQRVASPEETDAPEARESLIAIEVDRHSNPAELEEIEASLLEVLREVRTAVSD 192 RD + + V+ ++ D + ++ IEVDR S+ A+++ +E + VL +V +V+D Sbjct: 131 KRD-QGVITGVSYNDDKDESNDKVAVFLIEVDRLSSDADIKSLEKEIQSVLGDVAASVND 189 Query: 193 FDPMRAQARAAIEELEATRPAQVDPADHREAIEFLQWLLQDNFTFLGYDEYEVREDQGRQ 252 + M + I EL + RP + + EAI FL +L +FT LGY Y++ + +G Sbjct: 190 WQAMSNKLSETIAELPS-RPFPGEKRELDEAINFLTYLNNHHFTLLGYRRYDLHKVEGDL 248 Query: 253 RLDKVQNSELGVFRLD-QPRYRERIR-TDLGVEGDHYVPMPQLMSFAKSAHHARIHRPTY 310 L + LG+ + +P+ + + + L L+ KS +R+HRP Y Sbjct: 249 ELLPANETSLGLMNVPGKPKSSKGLMLSSLSDTARKEALDSSLLILTKSTEKSRVHRPAY 308 Query: 311 PDYISIDRYDDQGRVIGERRFLGMFTATVYNESPRNVPILRRKLQAVMDIAGFSPKGHNG 370 DYI I R+D+QG VIGE RF+G++ + +YN SPR +P+L K+Q V+D +G +P H+ Sbjct: 309 VDYIGIKRFDEQGNVIGEDRFIGLYASNLYNRSPREIPLLAEKIQRVLDDSGLTPHSHDY 368 Query: 371 KQLLQILEVYPRDDLFQIDIEELAQTALGILDIRERRRVRLFIREDTFGKFYSCLVFVPR 430 K L+ ILE PRD++ Q ELA A G+L++++R +++LF+R+D FG+F SCLV+V + Sbjct: 369 KALMHILETLPRDEIVQARESELASMAHGVLEMQDRDKLKLFVRKDGFGRFLSCLVYVSK 428 Query: 431 DVFSTELRVRLQELLCEELDATFG-DFNTYLSESVLARIQFILRFNGEKPVEYDIKRLEE 489 D ++T+LR Q +L + + +F TY SES LAR +I++ + + D+ +E Sbjct: 429 DRYNTKLREDTQRILAQHFNTKEDVEFTTYFSESTLARTHYIVKVDNNI-TDVDVAAIEN 487 Query: 490 KLVKLARNWRDDLLNASIEGFGEESANLLMSRFRDAFPASYREDFSARTAVYDLQHIGEL 549 L++ AR+W D L A I GEES N L+ R+ +AFP SY+ED +AV D++H+ L Sbjct: 488 NLIEAARSWEDKLNTALITAQGEESGNRLVKRYVNAFPRSYKEDVLPSSAVVDIEHLEAL 547 Query: 550 DEGAPLALSLYRLIEE--EGSGVNLKLFHRGAPIPLSDVLPMMENLGLRVIGERPYEVQA 607 D+ L + Y+ E + + V LKLFH+ PI LSDVLPM+EN GLRVI ERPYEV Sbjct: 548 DDDHKLGMLFYQPQETALKDNKVRLKLFHKDEPIHLSDVLPMLENFGLRVINERPYEVMT 607 Query: 608 SDAS-YWIHDFNLEHHTSVEMNLQEMRGPFIEAFQRIWAGEADNDAFNRLIIGANLDWRE 666 +D S +WI DF + + NL + + F A ++W E ++D FNRL++ L RE Sbjct: 608 ADGSTFWILDFLMTVQGAAVDNLADSQDRFQTALSQVWRKELEDDGFNRLVLATGLSGRE 667 Query: 667 VAMLRAYARYLKQIRFGMSQDYIATTLGSHPEITRELVSLFELRFDPA--ERPGEGDIEE 724 V++LRAYA+Y++QI SQ YI T S+P+I LV +F +F+P R +E+ Sbjct: 668 VSVLRAYAKYMRQIDATFSQAYIEETFSSYPQIADLLVKMFIRKFNPKLKTRTLAKFVEQ 727 Query: 725 CESRILTLLDEVPSLNDDQLLRRYMELIKATLRTNYYQRTEEGRYKDYLAFKLDPSQVSG 784 + R L++V SL+DD+++RRY++LI ATLRTN+YQ +G K Y++FK P ++ Sbjct: 728 IDMR----LEDVSSLDDDRIIRRYLDLINATLRTNFYQVLPDGSNKPYVSFKFSPEEIPE 783 Query: 785 IPKPCPAYEIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIV 844 +P+P P +EIFV SPRVEGVHLRGGKVARGGLRWSDR EDFRTEVLGLVKAQQVKN VIV Sbjct: 784 MPRPLPKFEIFVYSPRVEGVHLRGGKVARGGLRWSDRREDFRTEVLGLVKAQQVKNTVIV 843 Query: 845 PMGAKGGFVCKRMPEGADREATQKEGIACYQIFIRALLDVTDNLVGGEVVPPRDVVRHDD 904 P+GAKGGFVCK++P R+A EG CY++FIR LLD++DN+V GE+VPP +VVRHD+ Sbjct: 844 PVGAKGGFVCKQLPTEGGRDAFFTEGQECYRLFIRGLLDISDNIVEGEIVPPANVVRHDE 903 Query: 905 NDPYLVVAADKGTATFSDIANEISTEYGHWLGDAFASGGANGYDHKKMAITAKGAWESVK 964 +DPYLVVAADKGTATFSDIAN IS EYG WLGDAFASGG+NGYDHKKM ITA+GAWESVK Sbjct: 904 DDPYLVVAADKGTATFSDIANAISEEYGFWLGDAFASGGSNGYDHKKMGITARGAWESVK 963 Query: 965 RHFRGLGVNTQEDEFSVVGIGDMAGDVFGNGMLLSDKIRLVGAFNHLHIFVDPTPDAAAS 1024 RHFR +GV+ Q +F+ + IGDMAGDVFGNGMLLS+ RLV AFNH+HIF+DP PDAA+S Sbjct: 964 RHFREIGVDCQTTDFTCLAIGDMAGDVFGNGMLLSEHTRLVTAFNHMHIFIDPNPDAASS 1023 Query: 1025 FAERQRLFDMPRSSWEDYNTELISEGGGIFPRSAKSITITPQMKKVFGIREDKLSPNELI 1084 + ER RLF+MPRSSWEDYN +LIS+GGGIF RSAKSIT+TP+MKK+ ++ ++PNEL+ Sbjct: 1024 YKERARLFEMPRSSWEDYNKDLISKGGGIFLRSAKSITLTPEMKKMLDTKKASMTPNELL 1083 Query: 1085 RAMLVSKVDLVWNGGIGTYVKSSEETDAEVGDKANDALRIDGRELNCRVVGEGGNLGLTQ 1144 + +L KVDL+WNGGIGTY+K++ ET AEVGD+ANDALR++G E+ R++GEGGNLG TQ Sbjct: 1084 KELLKMKVDLIWNGGIGTYIKATSETHAEVGDRANDALRVNGNEVQARIIGEGGNLGCTQ 1143 Query: 1145 RGRMEAAAKGVRVNTDFIDNAGGVNCSDHEVNIKILIDEVVSRGDLTEKQRNQLLADMTD 1204 GR+E AA G R+NTDF+DN GGV+CSD+EVNIKIL++ +V+ G++T KQRN+LL +MTD Sbjct: 1144 LGRIEYAANGGRMNTDFVDNVGGVDCSDNEVNIKILLNAMVAEGEMTVKQRNRLLVEMTD 1203 Query: 1205 EVSELVLLDNYRQTQALDLAELLSRQGIGPYRRFISELEAAGQIDRELEFLPSDEELLER 1264 EVS +VL D QT+ + + ++ + + RFI LE ++DR LEFLP+D+EL ER Sbjct: 1204 EVSRIVLQDCKDQTRTISVTQVRGAEQLKEQIRFIHYLEKEDKLDRALEFLPTDDELAER 1263 Query: 1265 TQHNQGMTLPELSVLISYAKSVLKGDLIASDVPDDPTIMRFVERVFPSMLAERYRDEMYE 1324 + + +T PELSVL++YAK VLK L+ ++ DD + + + FP L E+Y + M Sbjct: 1264 LANGKSLTRPELSVLVAYAKMVLKEQLLTPEITDDSFLSQLLIEYFPRQLQEKYSERMVT 1323 Query: 1325 HRLKREIVATQVANDLVDYMGVVFVRRLMDSTGADRADIARAYVIARDSFQLPRLWEQIE 1384 H L+ EI+AT +AN+LV+ MG+ FV+R+ D TGA A+ A Y +AR+ F L L + I Sbjct: 1324 HPLRAEIIATSLANELVNDMGLNFVQRMQDETGASVAEAAICYTMAREVFGLAELTKSIT 1383 Query: 1385 ALDNKVPSQVQYSMMLDLMRMLRRSTRWFLRQRT-GMSTRDTIDYFAPRLAQLQENIGKR 1443 AL+ VP+ VQ M+ L R LRR+ RWFLR R S + +F+P +L++N+ + Sbjct: 1384 ALNGVVPAVVQGEMLHQLRRNLRRACRWFLRHRNRNQSIEQVVAFFSPVFQELRQNVHQY 1443 Query: 1444 LRGEEQEQWSARRQELVKAGVPEALASTVAAAGSLYAALGIIQTARQTDEKPQRVAEIFY 1503 L +E A LVK GVPE +A+ V +L++AL I Q A D+ VAE +Y Sbjct: 1444 LVEDEVNGIRAEIAALVKEGVPEQVATDVVNMSTLFSALDISQIAELEDKPVALVAETYY 1503 Query: 1504 EVGARLELPWIIQQVTRLEVRDGWQAKARDTFRDDIDRQQLALTASVLGMDGGPRDSAER 1563 ++GAR++L W ++Q++ V + WQA AR FR+++D QQ +L++ VL ++ Sbjct: 1504 KLGARIDLHWFLEQISAQPVANHWQALARAAFREELDWQQRSLSSVVLRTCPSVCEADAI 1563 Query: 1564 VDRWLSLHEGMHQRWRHLLEEVGSGSQGGFPLFAVAVREL 1603 +D+W+ ++G+ +RW H+L + + F F+VA+REL Sbjct: 1564 IDQWVESNQGLLERWFHMLADFKTSQTHEFAKFSVALREL 1603 Lambda K H 0.320 0.137 0.400 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: 5570 Number of extensions: 263 Number of successful extensions: 11 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: 1613 Length of database: 1614 Length adjustment: 51 Effective length of query: 1562 Effective length of database: 1563 Effective search space: 2441406 Effective search space used: 2441406 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