Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_086510711.1 BZY95_RS14990 NADP-specific glutamate dehydrogenase
Query= BRENDA::Q9TVN3 (438 letters) >NCBI__GCF_002151265.1:WP_086510711.1 Length = 450 Score = 453 bits (1166), Expect = e-132 Identities = 236/442 (53%), Positives = 301/442 (68%), Gaps = 6/442 (1%) Query: 1 MKDLEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWEND 60 ++ L +PAQ EF QA+ EV+E + ++ + P+Y ++ I+ERI EP F+V W +D Sbjct: 8 LEGLRKSSPAQSEFYQAAEEVLECLRPLLETVPRYHQHSIIERIVEPERQIMFRVSWVDD 67 Query: 61 KHEIMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGG 120 ++ VNKGYR+QFN+A+GPYKGGLRFH +V +KFLGFEQIFKN+LTGLP+GGGKGG Sbjct: 68 AGKVQVNKGYRVQFNSALGPYKGGLRFHPSVNASIIKFLGFEQIFKNALTGLPIGGGKGG 127 Query: 121 SDFDPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQH 180 S+FDP+GKSD EI+RFC+SFM L+++IG IDVPAGDIGVG REIGY++GQYKRLT + Sbjct: 128 SNFDPKGKSDGEIMRFCQSFMNELYRHIGATIDVPAGDIGVGAREIGYMYGQYKRLTGSY 187 Query: 181 EGVLTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLK 240 EGV TGKGLNWGGSL R EATG+G +YFA +L A GD I GKT +SG GNVA + K Sbjct: 188 EGVFTGKGLNWGGSLGRKEATGYGAVYFAQNMLEARGDSITGKTCLVSGAGNVAIYTIEK 247 Query: 241 AKQLGAKVVTISGPDGYIYDENGINTDEKINYMLEL-RASNNDVVA--PFAEKFGAKFIP 297 QLGA+ +T S G I+ GI+ E + + E+ R + + V P A A+ P Sbjct: 248 LYQLGARPITCSDSRGTIHHPEGIDL-ETLKLLKEVKRTTLREYVEYHPEATYIDAQDYP 306 Query: 298 --GKKPWEVPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRI 355 G W + ++AFP A QNE+ DA L NGV + E SNM TA AV F++ RI Sbjct: 307 SDGHAVWRIKGEVAFPSATQNEVTEADAMALLGNGVHCISEGSNMASTATAVDRFLEARI 366 Query: 356 VFAPGKAANAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYI 415 + PGKAANAGGVA S LEM+QNS W+ ++VD KL+ IM IH C +E Sbjct: 367 AYGPGKAANAGGVATSQLEMAQNSSMQQWSLKKVDTKLQAIMAGIHRQCAGTAEEFGEPT 426 Query: 416 NYVKGANIAGFKKVADAMVDLG 437 N V GANIAGF+KVADAM+D G Sbjct: 427 NLVLGANIAGFRKVADAMIDQG 448 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: 582 Number of extensions: 24 Number of successful extensions: 2 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: 450 Length adjustment: 32 Effective length of query: 406 Effective length of database: 418 Effective search space: 169708 Effective search space used: 169708 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