Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011780134.1 MVAN_RS14680 glutamine synthetase
Query= BRENDA::O07752 (450 letters) >NCBI__GCF_000015305.1:WP_011780134.1 Length = 442 Score = 402 bits (1034), Expect = e-117 Identities = 205/439 (46%), Positives = 280/439 (63%), Gaps = 7/439 (1%) Query: 11 IAQLEAEGVDTVIGTVVNPAGLTQAKTVPIRRTNTFANPGLGASPVWHTFCIDQCSIAFT 70 + L AEGV + G+V + AG+T+AK VP+ R FA G+G SP W FC+D IAFT Sbjct: 10 VGHLRAEGVAIIAGSVTDLAGVTRAKYVPVARLGAFARSGMGVSPSWSVFCVDS-GIAFT 68 Query: 71 ADISVVGDQRLRIDLSALRIIGDGLAWAPAGFFEQDGTPVPACSRGTLSRIEAALADAGI 130 I V GD R+RID LR++ G+AWAP +Q G P P C+R LSR+E A AD G+ Sbjct: 69 PTIGVAGDLRIRIDPEDLRVVDAGVAWAPGTLNDQHGHPAPLCTRTLLSRVERAAADRGL 128 Query: 131 DAVIGHEVEFLLVDADGQRLPSTLWAQYGVAGVLEHEAFVRDVNAAATAAGIAIEQFHPE 190 D +G E+E ++ ADG + W+ YG+ L+ AF+ D+ +A AG+ +EQ H E Sbjct: 129 DVRMGGELECTMLSADGGPATTEPWSPYGIRTSLDRSAFLVDLATSAERAGLPLEQLHTE 188 Query: 191 YGANQFEISLAPQPPVAAADQLVLTRLIIGRTARRHGLRVSLSPAPFAGSIGSGAHQHFS 250 YG +Q E+SLAP P AAAD ++L R+++GR A RHGLR+S SP PF G+ G+GAH H S Sbjct: 189 YGHDQLEVSLAPDTPTAAADAVILARIVLGRVAARHGLRISFSPVPFEGAAGNGAHLHLS 248 Query: 251 LTMSEGMLFSGGTGAAGMTSAGEAAVAGVLRGLPDAQGILCGSIVSGLRMRPGNWAGIYA 310 L+ ++G L SGG G G+ +AG A+AGVL LPD G+ GS S LR++PGNWAG A Sbjct: 249 LSDADGPLLSGGDGPHGLRTAGAQAIAGVLDTLPDLIGVYAGSAASALRLKPGNWAGATA 308 Query: 311 CWGTENREAAVRFVKGGAGSAYGGNVEVKVVDPSANPYLASAAILGLALDGMKTKAVLPS 370 CWG ENREAAVR + G+ +G N+E+K++D SANPYLA+AA LG AL G+ LP Sbjct: 309 CWGLENREAAVRLIAATPGNPHGANMELKLIDASANPYLAAAAFLGSALRGIGRHLELPE 368 Query: 371 ETTVDPTQLSDVDRDRAGILRLAADQADAIAVLDSSKLLRCILGDPVVDAVVAVRQLEHE 430 E +P Q S VD L Q +A+ +++S + +L +V+A+VAVR+ E + Sbjct: 369 EIPENPAQ-SGVDTP-----ALPLGQREALDAMETSDVAAELLTPAIVEALVAVRRYESK 422 Query: 431 RYGDLDPAQLADKFRMAWS 449 +G L PAQ+ D R+AW+ Sbjct: 423 TFGGLPPAQICDALRLAWT 441 Lambda K H 0.319 0.135 0.399 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: 653 Number of extensions: 33 Number of successful extensions: 3 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: 450 Length of database: 442 Length adjustment: 32 Effective length of query: 418 Effective length of database: 410 Effective search space: 171380 Effective search space used: 171380 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 (21.8 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