Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate 351498 BT1970 glutamate dehydrogenase (NCBI ptt file)
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__Btheta:351498 Length = 444 Score = 547 bits (1410), Expect = e-160 Identities = 268/445 (60%), Positives = 338/445 (75%), Gaps = 3/445 (0%) Query: 1 MKTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFR 60 M +++ L+ + P E E+ QAV+EVL ++EE YN+HPEF+K +IER+ PDRVF FR Sbjct: 1 MNAAKVLDDLKRRFPNEPEYHQAVEEVLSTIEEEYNKHPEFDKANLIERLCIPDRVFQFR 60 Query: 61 VPWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPM 120 V W+DD+G +Q N+GYRVQ NNAIGPYKGGIRFH SVNLSILKFL FEQ FKN+LTTLPM Sbjct: 61 VTWMDDKGNIQTNMGYRVQHNNAIGPYKGGIRFHASVNLSILKFLAFEQTFKNSLTTLPM 120 Query: 121 GGGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYK 180 GGGKGG+DFSP+GKS AE+MRF Q+FM ELWR+IGP+TD+PAGDIGVGGREVG+MFGMYK Sbjct: 121 GGGKGGSDFSPRGKSNAEVMRFVQAFMLELWRHIGPETDVPAGDIGVGGREVGFMFGMYK 180 Query: 181 KLAREHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVA 240 KLA E TGT TGKG EFGGS +RPE+TG+G +YF+ M K G D KGK +SG GNVA Sbjct: 181 KLAHEFTGTFTGKGREFGGSLIRPEATGYGNIYFLMEMLKTKGTDLKGKVCLVSGSGNVA 240 Query: 241 WGVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNA 300 +K ELG KVVT S DGY+YDPDGI+ EK +++L++ + +Y +++ Sbjct: 241 QYTIEKVIELGGKVVTCSDSDGYIYDPDGIDR-EKLDYIMELKNLYRGRIREYAEKY-GC 298 Query: 301 QFFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVAN 360 ++ G KPW +K D A+P ATQNE+N + A+ L NG V+E +NM T EA + Sbjct: 299 KYVEGAKPWGEKCDIALPSATQNELNGDHARQLVANGCIAVSEGANMPSTPEAVRVFQDA 358 Query: 361 KMLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGN- 419 K+L+APGKA NAGGVS SGLEMTQN++ L W+ EEVD+ L IM++IHE CV YG + + Sbjct: 359 KILYAPGKAANAGGVSVSGLEMTQNSIKLSWSAEEVDEKLKSIMKNIHEACVQYGTEADG 418 Query: 420 YIDYVKGANIAGFMKVAKAMVAQGV 444 Y++YVKGAN+AGFMKVAKAM+AQG+ Sbjct: 419 YVNYVKGANVAGFMKVAKAMMAQGI 443 Lambda K H 0.319 0.137 0.417 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: 715 Number of extensions: 34 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: 445 Length of database: 444 Length adjustment: 32 Effective length of query: 413 Effective length of database: 412 Effective search space: 170156 Effective search space used: 170156 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 (21.7 bits) S2: 51 (24.3 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