Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012566657.1 RC1_RS07005 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_000016185.1:WP_012566657.1 Length = 456 Score = 183 bits (464), Expect = 1e-50 Identities = 145/440 (32%), Positives = 205/440 (46%), Gaps = 22/440 (5%) Query: 22 DVDTVIVAFTDMQGRLAGKRIS----GRHFVDDIATRGVECCSYLLAVDVDLNTVPGYAM 77 DV V V D+ G GKR+ G+ + D +A G C++ AVD+ T+ M Sbjct: 19 DVQAVDVLLPDLCGVFRGKRVPIDELGKVWTDGVAIPG---CTF--AVDITGETIEETGM 73 Query: 78 ASWDTGYGDMVMTPDLSTLRLIPWLPGT-ALVIADLVWADGSEVAVSPRSILRRQLDRLK 136 S G D + P TL +PW V+ + G +PRS++ + L Sbjct: 74 -SQALGVPDRICLPVAGTLAPVPWAARPLGQVLTSMRGPQGEPFPYAPRSLVETLVGTLA 132 Query: 137 ARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNID----YAILASSRMEPLLRD 192 ARGL +A ELEF + R A+ ++P + D Y + E +L D Sbjct: 133 ARGLTPVIAVELEFYLIAGG-RGAFEPPRPPVSPKNGLPQDRTQVYGLAELEDFEAVLDD 191 Query: 193 IRLGMAGAGLRFEAVKGECNMGQQEIGFRY-DEALVTCDNHAIYKNGAKEIADQHGKSLT 251 I + E GQ EI + +AL D+ ++K K +A +HG T Sbjct: 192 ITAACRDQAIPAGTAIAEYGPGQYEITLSHRPDALRAADDAVLFKRAVKGVAQRHGFDAT 251 Query: 252 FMAK-YDEREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCY 310 FMAK Y ++ + H+H+S+ DG +FA + P G S R + G TL Sbjct: 252 FMAKPYRDQASSGMHVHMSVLDRDGRNIFA-AEDPAG-SEQLRWAIGGLAQTLPAAMALA 309 Query: 311 APTINSYKRFADSSFAPTALAWGLDNRTCALRV-VGHGQNIRVECRVPGGDVNQYLAVAA 369 AP NS++R S+APT AWG++NRT ALR+ G + RVE R+ G D N YL VA Sbjct: 310 APGANSWRRLQPGSYAPTVAAWGVNNRTAALRIPAGPPPSRRVEYRIAGADANPYLVVAG 369 Query: 370 LIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVAH 429 L+AG L+G++ + P GNAY GAD RLP A L + SA++R G+ V Sbjct: 370 LLAGLLHGLDGRIDPGPPAEGNAY-GADAPRLPTGWDAALDLLDGSAVLRRGLGDAFVDT 428 Query: 430 YLNNARVELAAFNAAVTDWE 449 Y+ R E F A VT E Sbjct: 429 YVITKRAEQRKFAAEVTPLE 448 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: 582 Number of extensions: 35 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: 456 Length adjustment: 33 Effective length of query: 424 Effective length of database: 423 Effective search space: 179352 Effective search space used: 179352 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 10 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