Align Probable NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2 (characterized)
to candidate 8500598 DvMF_1346 Glu/Leu/Phe/Val dehydrogenase (RefSeq)
Query= SwissProt::Q9USN5 (1106 letters) >FitnessBrowser__Miya:8500598 Length = 1017 Score = 285 bits (729), Expect = 1e-80 Identities = 210/598 (35%), Positives = 304/598 (50%), Gaps = 51/598 (8%) Query: 505 AKSATSLADEASTYSITPMSATALMDLIQKTCTNEEDVSVMEMFVKFNTHLLKTNFFQTT 564 A+ +L D +T AT ++ + +E + +V+ M +F H+L+TN+F T Sbjct: 382 ARFDPTLGDREATARRLEADATDAVNAV----ADERERAVLLMIQRFFRHVLRTNYFLDT 437 Query: 565 KVALSFRFDPSFLDST---QYKDPLYAMIMSIGNEFRGFHLRFRDVARGGIRLIKSANPE 621 LSFR DP FL + ++ + + GFH+R+RD+ARGG+R++ + E Sbjct: 438 IYGLSFRLDPEFLPPAYRYEGEELPFGIFFFHAPGGLGFHIRYRDMARGGVRVVPTRTQE 497 Query: 622 AFGLNARGLFDENYNLAKTQMLKNKDIPEGGAKGVILLGKDCQDKPELAFMKYIDSIIDL 681 F L + L+DE LA Q +KNKDIPEGGAK VILLG LA I+S++D+ Sbjct: 498 QFELESNRLYDEVKGLAYAQQVKNKDIPEGGAKAVILLGP--LGDVGLAVSSVINSLLDV 555 Query: 682 LIVNKSQP----LVDKLGKPEILFMGPDENTADL-VNWATIHAHRRNAPWWKSFFTGKKP 736 ++ + P +VD LG+ EI++ GPDEN + W A +R W +F + K Sbjct: 556 VLPGQDTPALPGVVDYLGREEIIYCGPDENIQPAHIAWMVERARQRGYRWPSAFMSSKAG 615 Query: 737 TMGGIPHDKYGMTSLSVRCYVEGIYKKLNITDP--SKLTKVQTGGPDGDLGSNEIKLSNE 794 GI H +YG+TS+ V + E + + L I DP T TGGP GD+ N ++L E Sbjct: 616 A--GINHKQYGVTSIGVMVFAEEMLRHLGI-DPFTQPFTVKLTGGPKGDVAGNLMRLMFE 672 Query: 795 KY------IAVIDGSGVLYDPAGLDRTELLRLADERKTIDHFDAGKLSPEGYRVLVKDTN 848 Y +AV DG G +DP GLDR ELLRL D +++I FD +L EG V V DT Sbjct: 673 TYGDNARIVAVSDGHGGAWDPDGLDRAELLRLVDAQRSISAFDPARLRGEGAWVAVSDT- 731 Query: 849 LKLPNGEIVRNGTIFRNTAHLRYKADTFVPCGGRPNAININNVEQLIDDHGRPAFKYLVE 908 P G VR NTAH AD F+P GGRP+ IN N D G P + ++E Sbjct: 732 ---PEG--VRRRNTLHNTAH----ADIFIPAGGRPDTINTRNWHDFFDRGGVPTARAVIE 782 Query: 909 GANLFITQDAKSVLEKAGVIVIRDASANKGGVTSSSLEVLASLSFDDASFKENMCVHDGK 968 GANLF+ +A+ L + GV+V+ +SANK GV SS EVL L D F H + Sbjct: 783 GANLFVAPEARKRLAERGVLVVHGSSANKTGVICSSYEVLGGLVMTDEEF----IAHKDR 838 Query: 969 VPTFYADYVNEVKRIIQRNANLEFEAIWKGHSENKIPYTSLSNHLSTEIVKLDHDIY--- 1025 F A+ ++ ++ + A L I + + S+ +S E+ + +Y Sbjct: 839 ---FVAEVLDILRVRARDEARLLLAEIRRCDGCKALHEISVD--VSLEMNAVADALYAAL 893 Query: 1026 --NYEKLWADVGFRNAVLRASIPKTLQAKIGLEKMLERIPESYLRAIFSTYLASRFVY 1081 E + AD R VL +P L + E++ ERIP + A+ + + ASR VY Sbjct: 894 MARGEPVEADPVLRQ-VLLGYLPPVLVERFP-ERIFERIPLRHQYALVAAHTASRIVY 949 Lambda K H 0.319 0.135 0.393 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: 2181 Number of extensions: 92 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 1106 Length of database: 1017 Length adjustment: 45 Effective length of query: 1061 Effective length of database: 972 Effective search space: 1031292 Effective search space used: 1031292 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: 58 (26.9 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