Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_076480672.1 BW971_RS14270 NAD-glutamate dehydrogenase
Query= BRENDA::A0R1C2 (1594 letters) >NCBI__GCF_900156495.1:WP_076480672.1 Length = 1591 Score = 1432 bits (3708), Expect = 0.0 Identities = 791/1573 (50%), Positives = 1027/1573 (65%), Gaps = 58/1573 (3%) Query: 43 VAAHYRLASMRAPGETKAAVYPGDAGSGAALQIVTDQAPMLVDSVTVLLHRHGIAYTAIM 102 V+ H +A+ R+PGE V GS + VTD P LV+ V+ L R G++ I Sbjct: 48 VSHHLSVAAQRSPGEVLVEVRAAARGS-ITVTTVTDDMPRLVEGVSSALGRLGLSVWRID 106 Query: 103 NPVFRVRRGLDGELLDVRP---AAEAAPGDGADECWILVPITAAADGEALTEATR-LVPG 158 +PV V R G+LL + A PG+ E WI V G A R V Sbjct: 107 HPVLSVWRDAAGQLLAIGTPDSADNGEPGERIAESWIHVEAQPIRPGSVDAPAVRDRVAE 166 Query: 159 ILAEARQIGLDSGAMIAALHGLANDLATDLEGHFPNAERKEVAALLRWLADGHFVLLGYQ 218 ++ + D AM L +A+ D G +P ALLRW+A G F +G+ Sbjct: 167 VIGRVVDVHRDHRAMTERLRTVADRCGADA-GQYP--------ALLRWMAGGMFAPIGWY 217 Query: 219 QCVVGDGNAEVDPASRLGVLRLRNDVLPPLTDSDDLLVLAQATM-----PSYLRYGAYPY 273 G E A+ GV R + P D D ++ Q + P+ + YP Sbjct: 218 TVDQITGAPE---AAGQGVWRSPDF---PRPDRDAVVTAEQPLIRRIHFPTAILRTDYPT 271 Query: 274 IVVVRE-SPGASRVIEHRFVGLFTVAAMNANALEIPLISRRVEEALAMAHRD-PSHPGQL 331 ++ V E + V EH F+G+ T A++ N LEIP++ RV +ALA+A D S+ GQ Sbjct: 272 LLQVAEVDDTGAPVREHVFIGVLTPTALHENVLEIPVVRERVADALAVAGADIDSYSGQA 331 Query: 332 LRDIIQTIPRPELFALSSKQLLEMALAVVDLGSRRRTLLFLRADHLAHFVSCLVYLPRDR 391 + +++Q P E+FA + QL +V+D R +FLR+D A +S L+YLPRD+ Sbjct: 332 MLELLQGYPLSEIFASDAGQLAANLRSVLDAVPGGRLRVFLRSDPHAETLSALIYLPRDK 391 Query: 392 YTTAVRLEMQDILVRELGGAGIDYSARVSESPWAVVHFTVRLPEGTAADSVDTSLENESR 451 Y T R +MQ +L E G I+Y+ RVS + A++H +R+P AA D + E + R Sbjct: 392 YNTRTRQQMQTLLRDEFGSEDIEYTVRVSVAAHALLHLLMRVP---AATGDDIAPEVQRR 448 Query: 452 IQDLLTEATRNWGDRMI--------SAAAAASISPAALEHYAHAFPEDYKQAFAPQDAIA 503 +QD L A+R W D + + + +A + P + HY + + YK+ P A+A Sbjct: 449 LQDALVAASRGWDDGLRELVDAGVQAGSTSAPVGPETIGHYIRSLGDGYKEERDPAAALA 508 Query: 504 DISLIEALQDDSVKLVLADTAEDRVWKLTWYLGGHSASLSELLPMLQSMGVVVLEERPFT 563 DI+ + L + L D VW+ YL G SA+L+++LP+LQS+GV VL+ERPF Sbjct: 509 DITRLATLAPGDFSVDLRRV--DDVWRFGLYLCGRSATLTDVLPVLQSLGVDVLDERPFE 566 Query: 564 LRRTDGLPVWIYQFKISPHPSI-----PHAPDAEAQRDTAQRFADAVTAIWHGRVEIDRF 618 + R DG IY+F +SP + P P A A R +A +A+W G +D F Sbjct: 567 VTRPDGERCRIYEFGLSPTSGMVIHDGPAQPGAGA---VETRVTEAFSAVWRGHAAVDSF 623 Query: 619 NELVMRAGLTWQQVVVLRAYAKYLRQAGFPYSQSHIESVLNENPHTTRSLIDLFEALFDP 678 NELV+R GL W+Q +LR+YA+YLRQ GF YS SH+ SVL + R L++LF FDP Sbjct: 624 NELVLRCGLDWRQAAMLRSYARYLRQCGFAYSASHVASVLGAHADICRGLVELFFGSFDP 683 Query: 679 SQETDGRRDAQGAAAAVAADIDALVSLDTDRVLRAFANLIEATLRTNYFVARPDSARARN 738 + RR QG A + + +VSLD DR++ AF +I AT+RTN+FV PD R Sbjct: 684 DGADEDRR--QGVVADLDEMVGDIVSLDADRIVSAFVAMIGATVRTNFFVTDPDDGGHRP 741 Query: 739 VLAFKLNPLVIKELPLPRPKFEIFVYSPRVEGVHLRFGFVARGGLRWSDRREDFRTEILG 798 VL+FKL P I + P PRP +EIFVYSPR+EGVHLRFG VARGGLRWSDRR+D+RTEILG Sbjct: 742 VLSFKLRPRDIPQTPQPRPLYEIFVYSPRIEGVHLRFGSVARGGLRWSDRRDDYRTEILG 801 Query: 799 LVKAQAVKNAVIVPVGAKGGFVVKRPPTLTGDAAADREATRAEGVECYRLFISGLLDVTD 858 LVKAQAVKNAVIVPVGAKGGFVVKRPP TGD A DR+A R EG+ CYR FI GLLD+TD Sbjct: 802 LVKAQAVKNAVIVPVGAKGGFVVKRPPAATGDPAVDRDAFRQEGIACYRRFIGGLLDITD 861 Query: 859 NVDKATGAVVTPPEVVRRDGEDAYLVVAADKGTATFSDIANEVAKSYGFWLGDAFASGGS 918 N+D++TG V+ VVRRDG+D YLVVAADKGTATFSDIAN+VA Y FWLGDAFASGGS Sbjct: 862 NLDRSTGEVLPARSVVRRDGDDTYLVVAADKGTATFSDIANDVAAGYDFWLGDAFASGGS 921 Query: 919 IGYDHKAMGITAKGAWESVKRHFREMGVDTQTQDFTVVGIGDMSGDVFGNGMLLSKHIRL 978 GYDHK MGITA+GAWE+V+RHFREMGVDTQ++DF VVG+GDMSGDVFGNGMLLSKHIRL Sbjct: 922 AGYDHKVMGITARGAWEAVRRHFREMGVDTQSEDFAVVGVGDMSGDVFGNGMLLSKHIRL 981 Query: 979 VAAFDHRDIFLDPNPDAGRSWDERKRLFDLPRSSWADYDKSLISEGGGVYSRQQKSIPIS 1038 VAAFDHR +F+DP+PDA S+ ER+RLFDLPRSSWADYD +LIS GGGV+SR KSIPIS Sbjct: 982 VAAFDHRHVFIDPDPDAATSYVERRRLFDLPRSSWADYDPALISTGGGVWSRDLKSIPIS 1041 Query: 1039 PQVRTALGLDADVEELTPPALIKAILKAPVDLLWNGGIGTYIKAETEADADVGDRANDQI 1098 Q+R ALGLD V L+PP L++AIL APVDLLWNGGIGTY+KA E++ DVGD+AND I Sbjct: 1042 AQIRAALGLDDGVTALSPPDLMRAILTAPVDLLWNGGIGTYVKASGESNDDVGDKANDAI 1101 Query: 1099 RVCGNQVRAKVIGEGGNLGVTALGRIEFDLAGGRINTDALDNSAGVDCSDHEVNIKILID 1158 RV G+QVRAKVIGEGGNLGVTA GRIEFDL+GGR+NTDA+DNSAGVDCSDHEVNIKIL+D Sbjct: 1102 RVNGDQVRAKVIGEGGNLGVTARGRIEFDLSGGRVNTDAMDNSAGVDCSDHEVNIKILLD 1161 Query: 1159 SAVTAGKVTPEERTELLLSMTDEVGELVLADNRDQNDLMGTSRANAASLLSVHARMIKDL 1218 + V++G + +R LL SMTDEVG+LVLADN QN +G +RA A + VH R++++L Sbjct: 1162 AQVSSGALAAADRNPLLESMTDEVGDLVLADNISQNAELGLARAGAGQSVDVHVRLLREL 1221 Query: 1219 VDNRGLNRELEALPSEKEIRRRADAG-----IGLTSPELATLMAHVKLALKDDVLASDLP 1273 G++ ELEALP+ +R+R A GLTSPELAT++AHVKL LK D+L+++LP Sbjct: 1222 AGTYGVDLELEALPTVAALRKRVAASDSSRPSGLTSPELATVLAHVKLGLKSDLLSTELP 1281 Query: 1274 DQEVFASRLPYYFPTRLREELHGEIRSHQLRREIITTMLVNDLVDTAGISYAYRITEDVG 1333 D EVF RL YFP LRE I H+LRR+I+TT LVND+VD AGI++A+R+ E Sbjct: 1282 DGEVFGPRLHAYFPLPLRERFAEGIAEHRLRRQIVTTSLVNDVVDKAGITHAFRLAEGAM 1341 Query: 1334 VGPVDAVRSYVAINAIFGIGDVWRRIRAAGDAGVPTSVTDRMTLDLRRLVDRAGRWLLNY 1393 P+D VR+YV ++ +F + D+W RI A D GV D M RRL+ RA RW+L Sbjct: 1342 CSPIDVVRAYVVVSTVFALDDLWARIEAV-DGGV--VAIDEMMTYTRRLLFRASRWMLAN 1398 Query: 1394 RPQPLAVGAEINRFGAKVAALTPRMSEWLRGDDKAIVSKEAGDFASHGVPEDLAYHIATG 1453 RPQPL + AEI R+ +V L+PR+ WL +A V+ + + GV E LA Sbjct: 1399 RPQPLPIAAEITRYARRVQDLSPRVPGWLGPGSRADVATRVDAWVADGVDESLAADAGVS 1458 Query: 1454 LYQYSLLDVIDIADIVDREPDEVADTYFALMDHLGADALLTAVSRLSRDDRWHSLARLAI 1513 L+++ LLD+ID A+I DR+ EV + YF ++D LG + LLTAVSRL R DRWH+LARLA+ Sbjct: 1459 LHRFCLLDIIDAAEIADRDEIEVGELYFTVLDDLGVEGLLTAVSRLDRGDRWHALARLAL 1518 Query: 1514 RDDIYGSLRALCFDVLAVGEPDENGEEKIAEWETTNSSRVTRARRTLTEIYKDGEQDLAT 1573 RDD++ +R+LC ++ VGEP E+ ++I+EW+T ++SR+ R R L +I + G+ DLAT Sbjct: 1519 RDDLHAVVRSLCLQIMEVGEPGESPRQQISEWQTHHASRLARVRAVLDDIAETGDYDLAT 1578 Query: 1574 LSVAARQIRSMTR 1586 LSVAARQ+RS+ R Sbjct: 1579 LSVAARQLRSVIR 1591 Lambda K H 0.319 0.136 0.395 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: 6290 Number of extensions: 313 Number of successful extensions: 12 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: 1594 Length of database: 1591 Length adjustment: 51 Effective length of query: 1543 Effective length of database: 1540 Effective search space: 2376220 Effective search space used: 2376220 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 24 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