Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf1N1B4_4245 glutamine synthetase family protein
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4245 Length = 457 Score = 379 bits (974), Expect = e-110 Identities = 204/454 (44%), Positives = 276/454 (60%), Gaps = 5/454 (1%) Query: 7 PPLAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVD 66 P L++ L+R A+G++DTV+V DMQGRL GKR F+D CC+YLLA D Sbjct: 4 PLLSFDALKRAAASGEIDTVLVCMVDMQGRLVGKRFQVEFFIDS-GHEETHCCNYLLADD 62 Query: 67 VDLNTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLV-WADGSEVAVSPR 125 +D+ VPGYA ASW GYGD V+ PD++TLR +PWL TALV+ D++ ++ SPR Sbjct: 63 IDMEPVPGYAAASWSKGYGDFVLKPDMATLRRVPWLECTALVLCDVLDHHHRRDLPHSPR 122 Query: 126 SILRRQLDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSR 185 +IL++Q++RL+ RG A+ELEF +FD+ Y Y A Y DY IL ++R Sbjct: 123 AILKKQVERLRERGYTGMFASELEFYLFDESYEAIHERNYHKPKTAGHYIEDYNILQTTR 182 Query: 186 MEPLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQ 245 EP+LR IR + G+ E KGE GQ+EI RY +AL D+H I K+ KEIA Sbjct: 183 EEPVLRAIRKHLQACGIPVENSKGEWGPGQEEINIRYADALTMADHHVIIKHACKEIAQL 242 Query: 246 HGKSLTFMAKYD-EREGNSCHIHVSLRGTDG-SAVFADSNGPHGMSSMFRSFVAGQLATL 303 GK++TFMAK+ + G+S H+H SL +G ++F D GMS + RS+VAGQL Sbjct: 243 QGKAITFMAKWRYDAAGSSSHVHNSLWDKNGKKSLFFDPKAEFGMSKLMRSWVAGQLKYA 302 Query: 304 REFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN-IRVECRVPGGDVN 362 + T AP INSYKRF +FAPT W DNRT R+ G IR+ECR+ G D+N Sbjct: 303 NDITCFLAPYINSYKRFQAGTFAPTRAVWSRDNRTAGFRLCAEGSKAIRIECRIGGADLN 362 Query: 363 QYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAF 422 YLA AALIA GL GI+ L L P G+AY + + TL +A + S+++REAF Sbjct: 363 PYLAFAALIAAGLAGIDEKLSLTPPFEGDAYVDEHLPEVSKTLREACAALKASSMLREAF 422 Query: 423 GEDVVAHYLNNARVELAAFNAAVTDWERIRGFER 456 G++V+ HY++ A E ++ +TDWE RGFER Sbjct: 423 GDEVIDHYVHTAEWEQKEYDRRITDWELQRGFER 456 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: 595 Number of extensions: 23 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: 457 Length adjustment: 33 Effective length of query: 424 Effective length of database: 424 Effective search space: 179776 Effective search space used: 179776 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 Jul 25 2024. The underlying query database was built on Jul 25 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