Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf6N2E2_5686 glutamine synthetase family protein
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5686 Length = 447 Score = 181 bits (458), Expect = 6e-50 Identities = 143/462 (30%), Positives = 216/462 (46%), Gaps = 34/462 (7%) Query: 1 MTGPGSPPLAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCS 60 MT G LA +RL +++ V D+ G GK ++ F++ + Sbjct: 1 MTTDGQRSLA----QRLTGIDEIECVT---PDLNGVPRGKVMTAEGFLEGRRLQ------ 47 Query: 61 YLLAVDVDLNTVPGYAMAS--WDTGYGDMVMTPDLSTLRLIPWLPGT-ALVIADLVWADG 117 LA V L + G S + + GD+ + D + +PW AL I D G Sbjct: 48 --LARGVLLQCIMGGYPPSRFYGSDDGDLALVADPKQIHRLPWSQQPRALAICDADELTG 105 Query: 118 SEVAVSPRSILRRQLDRLKARGLVADVATELEFIVF------DQPYRQAWASGYRGLTPA 171 +S R L+ + R A GL VATELEF VF QP++ R Sbjct: 106 ESSRLSTRGQLKAVVARYAALGLAPVVATELEFFVFAPNPDPTQPFQPPMGLDGR----R 161 Query: 172 SDYNIDYAILASSRMEPLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDN 231 D + +++ +++ + P ++ MA GL + E + Q EI + + L+ D Sbjct: 162 EDGHSAFSVSSNNGLRPFFSEVYACMAALGLPRDTFMHEMGVSQFEINLLHGDPLLLADQ 221 Query: 232 HAIYKNGAKEIADQHGKSLTFMAK-YDEREGNSCHIHVSL-RGTDGSAVFADSNGPHGMS 289 ++K+ KE+A +HG ++ MAK G+S HIH S+ G VF+D G + Sbjct: 222 TFLFKHLLKEVALKHGLTVVCMAKPLAHTPGSSMHIHQSVVEEGSGRNVFSDEAGEP--T 279 Query: 290 SMFRSFVAGQLATLREFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN 349 + FR F+ GQ A L +FT +AP +NSY+R +P W DNR+ LR+ Sbjct: 280 AAFRHFIGGQQACLADFTALFAPNVNSYQRLCHPFASPNNACWSHDNRSAGLRIPASSPV 339 Query: 350 I-RVECRVPGGDVNQYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADA 408 RVE R+PG D N YLA+AA +A GLYGIE L+ P + ++ D LP TL A Sbjct: 340 ARRVENRLPGADANPYLAIAASLAAGLYGIEHRLE-PSAAIQGEFEVPDNLSLPCTLHAA 398 Query: 409 AVLFEDSALVREAFGEDVVAHYLNNARVELAAFNAAVTDWER 450 + S L +E FG + + Y+ + +EL +F +T WER Sbjct: 399 LERLKRSHLAKELFGTEFIEGYIASKTLELTSFFDEITPWER 440 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: 533 Number of extensions: 36 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: 447 Length adjustment: 33 Effective length of query: 424 Effective length of database: 414 Effective search space: 175536 Effective search space used: 175536 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