Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate AO356_01510 AO356_01510 glutamine synthetase
Query= BRENDA::O07752 (450 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01510 Length = 450 Score = 166 bits (419), Expect = 2e-45 Identities = 147/453 (32%), Positives = 213/453 (47%), Gaps = 27/453 (5%) Query: 7 AAAAIAQLEAEGVDTVIGTVVNPAGLTQAKTVPIRRTNTFANPGLGASPVWHTFCIDQCS 66 AAA +A L V T++ T + G+T+ ++ P + G G P ++ Q Sbjct: 6 AAALLAPLP---VTTLVTTDL--IGVTRGRSFPSDELPHYVTAGCGWVPA-NSALTPQDV 59 Query: 67 IAFTADISVVGDQRLRIDLSALRIIGDGL-AWAPAGFF------EQDGTPVPACSRGTLS 119 IA T GD RL DLS+ + +G A APA F E DG P AC R L Sbjct: 60 IASTNPWGAYGDLRLVPDLSSRVTVNNGPDAQAPALDFIHCDIRETDGRPWSACPRTLLQ 119 Query: 120 -RIEAALADAGIDAVIGHEVEFLLVDADGQ--RLPSTLWAQYGVAGVLEHEAFVRDVNAA 176 +E ++ G+ E EF L A Q RL +L AQ AG F + +A Sbjct: 120 DEVERYRSELGLQVFAAFEHEFNLAAAPAQPDRLAFSLQAQRQQAG------FAGWLLSA 173 Query: 177 ATAAGIAIEQFHPEYGANQFEISLAPQPPVAAADQLVLTRLIIGRTARRHGLRVSLSPAP 236 A G+ E F PEYG Q+EI+ P VAAAD+ V R I AR+ GL VS +P Sbjct: 174 LRAGGVEPEMFLPEYGKQQYEITCRPTLGVAAADRAVNVREITREIARQMGLDVSFAPKT 233 Query: 237 FAGSIGSGAHQHFSL-TMSEGMLFSGGTGAAGMTSAGEAAVAGVLRGLPDAQGILCGSIV 295 ++ +G H H SL +S + + G++S G+ AGVL LP + + + Sbjct: 234 SENAVCNGVHLHLSLQDLSADPVLHDAASSNGLSSLGQHWAAGVLHYLPALCALTAPTPL 293 Query: 296 SGLRMRPGNWAGIYACWGTENREAAVRFVK----GGAGSAYGGNVEVKVVDPSANPYLAS 351 S R++P +W+ YAC G NREAA+R GG A N+E + +D +A+P+LA Sbjct: 294 SYERLQPHHWSASYACLGQRNREAALRICPTVSLGGKPLANQYNLEFRAMDATASPHLAM 353 Query: 352 AAILGLALDGMKTKAVLPSETTVDPTQLSDVDRDRAGILRLAADQADAIAVLDSSKLLRC 411 AA+L G++ + L + T P +L + R GI+ L A A+ L S L Sbjct: 354 AALLIAGRLGIQHRWALNAVTDEIPDELDETQRRARGIIALPTTLAQALDCLRHSGALLE 413 Query: 412 ILGDPVVDAVVAVRQLEHERYGDLDPAQLADKF 444 L P+V+ A++ E L PA+ + + Sbjct: 414 ALPGPLVETYFALKAQEQALTQALSPAERCEHY 446 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: 444 Number of extensions: 27 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: 450 Length adjustment: 33 Effective length of query: 417 Effective length of database: 417 Effective search space: 173889 Effective search space used: 173889 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 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