Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate SMa0228 SMa0228 glutamate dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__Smeli:SMa0228 Length = 448 Score = 462 bits (1190), Expect = e-135 Identities = 237/446 (53%), Positives = 309/446 (69%), Gaps = 7/446 (1%) Query: 2 KTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRV 61 K + I+ + ++ GE EF QAV+EVL S+ V +HP + +N +IERI EP+R FRV Sbjct: 6 KLEPILAEVLRRNGGEHEFHQAVREVLESLGRVIAKHPRYAENALIERICEPERQIIFRV 65 Query: 62 PWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMG 121 PWVDD+G+VQ+N G+RVQFN+A+GPYKGGIRFHPSVN+ I+KFLGFEQ FKNALT +P+G Sbjct: 66 PWVDDKGQVQINRGFRVQFNSALGPYKGGIRFHPSVNIGIIKFLGFEQTFKNALTGMPIG 125 Query: 122 GGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKK 181 GGKGG+DF+P+G+S+ EIMRFCQS MTEL R++G TD+PAGDIGVGGRE+GYMFG YK+ Sbjct: 126 GGKGGSDFNPRGRSDGEIMRFCQSLMTELHRHLGEYTDVPAGDIGVGGREIGYMFGQYKR 185 Query: 182 LA-REHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVA 240 L R G LTGK +GGSR R E+TG+GA YFVQ M G+D++GK + +SG GNVA Sbjct: 186 LTNRYEAGVLTGKALFYGGSRARKEATGYGATYFVQRMIATKGLDFEGKRVTVSGSGNVA 245 Query: 241 WGVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVK-RFPN 299 +K E G K+V S +GYV D DGI+ + ++++ + +S+Y + + Sbjct: 246 IYTMEKVIEFGGKIVACSDSNGYVVDEDGID----LELVKEIKEVRRERISEYARLKGAG 301 Query: 300 AQFFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVA 359 + W+ D AMP ATQNE+ +DA+TL KNGV V E +NM CT EA + Sbjct: 302 THYIEAGSVWDVPCDVAMPSATQNELTGKDARTLVKNGVLAVGEGANMPCTPEAVRIFQE 361 Query: 360 NKMLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKD-G 418 +LFAPGKA NAGGV+ S LEM QNA WT E+ + L IMQ IH++C ++ G Sbjct: 362 AGVLFAPGKAANAGGVATSALEMQQNASRDSWTFEQTEARLATIMQAIHDRCAETAEEYG 421 Query: 419 NYIDYVKGANIAGFMKVAKAMVAQGV 444 DYV GANIAGF++VA+AM A GV Sbjct: 422 TPGDYVLGANIAGFVRVAEAMDALGV 447 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: 675 Number of extensions: 33 Number of successful extensions: 5 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: 448 Length adjustment: 33 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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