Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate PfGW456L13_1993 glutamine synthetase family protein
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1993 Length = 448 Score = 182 bits (462), Expect = 2e-50 Identities = 140/437 (32%), Positives = 209/437 (47%), Gaps = 20/437 (4%) Query: 23 VDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAMASWDT 82 +D V D+ G GK ++ F+D R ++ +L + P S D Sbjct: 16 IDQVECVTPDLNGVPRGKVMTSEGFLDG---RRLQMARGVLLQCIMGGYPPARFYGSDD- 71 Query: 83 GYGDMVMTPDLSTLRLIPWL-PGTALVIADL-VWADGSEVAVSPRSILRRQLDRLKARGL 140 GD+ + PD + + +PW P AL I D + +S R L+ + R ARGL Sbjct: 72 --GDLALIPDPAQIHRLPWSHPPRALAICDADELGTTTSSNLSTRGQLKAVIARYAARGL 129 Query: 141 VADVATELEFIVF----DQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLRDIRLG 196 VATELEF VF D G G D +++ +++ + P ++ Sbjct: 130 APVVATELEFFVFAPNTDPTLAFQPPLGLDGRR--EDGQSAFSVSSNNGLRPFFNEVYEC 187 Query: 197 MAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAK- 255 MA GL + E + Q EI + + L+ D ++K+ KE+A +HG S+ MAK Sbjct: 188 MAALGLPRDTFMHEMGVSQFEINLLHGDPLLLADQTFLFKHLLKEVALKHGLSVVCMAKP 247 Query: 256 YDEREGNSCHIHVSLRGTD-GSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTI 314 G+S HIH S+ D G VF+D G ++ FR F+AGQ + +FT +AP + Sbjct: 248 LAHTPGSSMHIHQSVVEIDSGRNVFSDEAGQE--TATFRHFIAGQQTCMADFTALFAPNV 305 Query: 315 NSYKRFADSSFAPTALAWGLDNRTCALRV-VGHGQNIRVECRVPGGDVNQYLAVAALIAG 373 NSY+R +P W DNR LR+ RVE R+PG D N YLA+AA +A Sbjct: 306 NSYQRLCHPYASPNNACWSYDNRAAGLRIPASLPVARRVENRLPGADANPYLAIAASLAA 365 Query: 374 GLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAHYLNN 433 GL+GIE+ L+ P G ++ D LP TL A + S L +E FG + + Y+ + Sbjct: 366 GLHGIEKTLEPSAPIQGE-FEVPDNLSLPCTLHAALERLKRSQLAKELFGAEFIEGYIAS 424 Query: 434 ARVELAAFNAAVTDWER 450 +EL +F+ +T WER Sbjct: 425 KTLELTSFHDEITPWER 441 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: 541 Number of extensions: 38 Number of successful extensions: 6 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: 448 Length adjustment: 33 Effective length of query: 424 Effective length of database: 415 Effective search space: 175960 Effective search space used: 175960 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