Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase II; GSII; EC 6.3.1.2 (characterized)
to candidate SM_b20745 SM_b20745 glutatmine synthetase II protein
Query= SwissProt::Q02154 (326 letters) >FitnessBrowser__Smeli:SM_b20745 Length = 344 Score = 609 bits (1571), Expect = e-179 Identities = 284/325 (87%), Positives = 303/325 (93%), Gaps = 3/325 (0%) Query: 1 MTKFKLEYIWLDGYTPVPNLRGKTQIKEFDEFPTLEQLPLWGFDGSSTMQAEG-SSDCVL 59 MTK+KLEYIWLDGYTPVPNLRGKTQIKEFD FPTLEQLPLWGFDGSST QAEG SSDCVL Sbjct: 1 MTKYKLEYIWLDGYTPVPNLRGKTQIKEFDAFPTLEQLPLWGFDGSSTQQAEGRSSDCVL 60 Query: 60 KPVAIYPDPARTNGALVMCEVMMPDGHA-HASNARATILDDEDAWFGFEQEYFFYQNGRP 118 KPVA+YPDP RTNGALVMCEVMMPDG H SN RAT+LDDE AWFGFEQEYFFY+NGRP Sbjct: 61 KPVAVYPDPVRTNGALVMCEVMMPDGKTPHPSNTRATVLDDESAWFGFEQEYFFYKNGRP 120 Query: 119 LGFPEQGYPAPQ-PYYTGVGYSNVGDVAREIVEEHLDLCLAAGINHEGINAEVAKGQWEF 177 LGFPEQGYPAPQ PYYTGVGY NVGD+AR+IVEEHLD+CLAAGINHEGINAEVAKGQWEF Sbjct: 121 LGFPEQGYPAPQGPYYTGVGYKNVGDIARQIVEEHLDICLAAGINHEGINAEVAKGQWEF 180 Query: 178 QIFGKGSKKAADQIWMARYLLQRLTEKYGIDIEYHCKPLGDTDWNGSGMHCNFSTKYLRE 237 Q+FGKGSKKAAD++W+ARYLL RLTEKYGID+E+HCKPLGDTDWNGSGMH NFST YLRE Sbjct: 181 QVFGKGSKKAADEVWLARYLLLRLTEKYGIDVEFHCKPLGDTDWNGSGMHANFSTAYLRE 240 Query: 238 VGGKEYFEALMASSDKNLMDHIAVYGPDNDKRLTGKHETAPWNKFSYGVADRGASIRVPH 297 VGGK+YFEALMA+ +KNL DHI VYGPDN RLTGKHETAPW+KFSYGVADRGASIRVPH Sbjct: 241 VGGKDYFEALMAAFEKNLHDHINVYGPDNHLRLTGKHETAPWDKFSYGVADRGASIRVPH 300 Query: 298 SFIKNDYKGYLEDRRPNSQGDPYQI 322 SF+ N Y+GYLEDRRPNSQGDPYQI Sbjct: 301 SFVNNGYRGYLEDRRPNSQGDPYQI 325 Lambda K H 0.319 0.138 0.438 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: 569 Number of extensions: 12 Number of successful extensions: 4 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: 326 Length of database: 344 Length adjustment: 28 Effective length of query: 298 Effective length of database: 316 Effective search space: 94168 Effective search space used: 94168 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 (21.7 bits) S2: 49 (23.5 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