Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_009123247.1 BUB52_RS02020 NADP-specific glutamate dehydrogenase
Query= BRENDA::Q9TVN3 (438 letters) >NCBI__GCF_900129655.1:WP_009123247.1 Length = 445 Score = 595 bits (1535), Expect = e-175 Identities = 285/438 (65%), Positives = 352/438 (80%), Gaps = 2/438 (0%) Query: 1 MKDLEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWEND 60 M LEA++P + E++QA +EV+ SI D+ N +P++ + KI+ER+ EP+ I F+V W +D Sbjct: 7 MSSLEAKHPGESEYLQAVKEVLLSIEDIYNQHPEFEKAKIIERLVEPDRIFTFRVTWVDD 66 Query: 61 KHEIMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGG 120 K E+ N GYR+QFNNAIGPYKGG+RFH +V L LKFLGFEQ FKN+LT LPMGGGKGG Sbjct: 67 KGEVQTNLGYRVQFNNAIGPYKGGIRFHASVNLSILKFLGFEQTFKNALTTLPMGGGKGG 126 Query: 121 SDFDPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQH 180 SDF PRGKSDAE++RFC++FM L++++GP++DVPAGDIGVGGRE+GY+FG YK+LT++ Sbjct: 127 SDFSPRGKSDAEVMRFCQAFMLELWRHLGPDMDVPAGDIGVGGREVGYMFGMYKKLTREF 186 Query: 181 EGVLTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLK 240 G TGKGL +GGSL+RPEATGFG +YF +++L G DIKGKT+AISGFGNVA+GA K Sbjct: 187 TGTFTGKGLEFGGSLIRPEATGFGGLYFVHQMLETKGIDIKGKTVAISGFGNVAWGAATK 246 Query: 241 AKQLGAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFAEKF-GAKFIPGK 299 A QLGAKV+TISGPDGYIYD NGI + EKI+YMLELRAS ND+VAP+A++F G+ F+PGK Sbjct: 247 ATQLGAKVITISGPDGYIYDPNGI-SGEKIDYMLELRASGNDIVAPYADEFPGSTFVPGK 305 Query: 300 KPWEVPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAP 359 +PWEV D+A PCA QNELN EDA L N V V E SNMGCT +A+ FI+N+I++AP Sbjct: 306 RPWEVKADIALPCATQNELNGEDAQHLIDNKVTCVGEISNMGCTPEAIDLFIENKIMYAP 365 Query: 360 GKAANAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVK 419 GKA NAGGVA SGLEMSQN+M ++W+A EVD KL IM IH CVK G E DGYINYVK Sbjct: 366 GKAVNAGGVATSGLEMSQNAMHISWSAAEVDEKLHAIMHGIHTQCVKYGTEPDGYINYVK 425 Query: 420 GANIAGFKKVADAMVDLG 437 GANIAGF KVA AM+ G Sbjct: 426 GANIAGFMKVAHAMMGQG 443 Lambda K H 0.317 0.137 0.405 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: 679 Number of extensions: 30 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: 438 Length of database: 445 Length adjustment: 32 Effective length of query: 406 Effective length of database: 413 Effective search space: 167678 Effective search space used: 167678 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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