Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate PP_4399 PP_4399 putative Glutamine synthetase
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Putida:PP_4399 Length = 413 Score = 186 bits (471), Expect = 2e-51 Identities = 129/377 (34%), Positives = 190/377 (50%), Gaps = 19/377 (5%) Query: 85 GDMVMTPDLSTLRLIPWLP-GTALVIADLVWADGSEVAVSPRSILRRQLDRLKARGLVAD 143 GD+ + + S + +PW G AL I D DG A+S R L+ + R A GL Sbjct: 38 GDLALVAEPSQVHRLPWSDDGRALAICDANELDGRPSALSTRGQLKAVIARYAALGLAPV 97 Query: 144 VATELEFIVF------DQPYRQAWAS-GYRGLTPASDYNIDYAILASSRMEPLLRDIRLG 196 VATELEF VF QP+ S G R L ++ +++ +++ + P +++ Sbjct: 98 VATELEFFVFAPNTDPQQPFLPPVGSDGRRELGHSA-----FSVSSNNGLRPFFKEVYHC 152 Query: 197 MAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAKY 256 MA GL + E + Q EI + + L+ D ++K+ KE+A +HG ++ MAK Sbjct: 153 MAALGLPRDTFMHEMGVSQFEINLLHGDPLLLADQTFLFKHLLKEVALKHGLTVVCMAKP 212 Query: 257 DERE-GNSCHIHVSL-RGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTI 314 R G+S HIH SL G VF+D G + F F+ G A + +FT +AP + Sbjct: 213 LARTPGSSMHIHQSLVEAGSGRNVFSDEQGLP--TETFHHFIGGLQACMADFTALFAPNV 270 Query: 315 NSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQNI-RVECRVPGGDVNQYLAVAALIAG 373 NSY+R +P W DNR LR+ RVE R+PG D N YLA+AA +A Sbjct: 271 NSYQRLCHPYASPNNACWSEDNRAAGLRIPASAPVARRVENRLPGADANPYLAIAASLAA 330 Query: 374 GLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHYLNN 433 GL+GIE+ LQ P P + ++ + LP TL A + S L RE FG + + Y+ + Sbjct: 331 GLHGIEQRLQ-PSPAIQGEFEVPEHLSLPCTLHAALERLKRSTLARELFGSEFIEGYIAS 389 Query: 434 ARVELAAFNAAVTDWER 450 +EL+ F +T WER Sbjct: 390 KTLELSDFFDEITPWER 406 Lambda K H 0.321 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: 497 Number of extensions: 38 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: 457 Length of database: 413 Length adjustment: 32 Effective length of query: 425 Effective length of database: 381 Effective search space: 161925 Effective search space used: 161925 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 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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