Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate Pf1N1B4_5853 Glutamine synthetase (EC 6.3.1.2), putative
Query= BRENDA::F2RM17 (446 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5853 Length = 443 Score = 166 bits (420), Expect = 1e-45 Identities = 129/411 (31%), Positives = 190/411 (46%), Gaps = 18/411 (4%) Query: 27 GHTHGHSVKRAHLEDALESGIQLPKLIQSFNALGMRVKDADFDAVGEVRLVPDRSTFRVL 86 G T G S LE +G + + + A G++RL+PD S+ + Sbjct: 20 GVTRGRSFPTDELEAYRVAGCGWVPANSALTPQDIIASSNPWGAYGDLRLIPDLSSRVTV 79 Query: 87 DHEDSVAAVCCSLYEID----DQTPWAADPRSALSGFISTLADD-DVVPSTALESEFHFY 141 ++ A D D PW A PR+ L + + + + A E EF+ Sbjct: 80 NNGPDANAPALDFIHGDIRETDGRPWGACPRTLLRNEVERYRSELGLQINAAFEHEFNLG 139 Query: 142 TSEDGDDEPHGTRGLYATASMREFNDIVLETIDALEAQQINVKKHCPEYAAGQHELVTKH 201 + H L A EF +L AL A + + PEY Q+E+ + Sbjct: 140 SGA----AEHLAFSLEAQRQGAEFGGWLLS---ALRAGGVEPEMFLPEYGKHQYEITCRP 192 Query: 202 REGLTPVDDYVFLRETVAAIAESHGFETTFLPFPFETAT-NGCHINLSLWNDTN--LFAP 258 G+ D V LRE IA G + +F P E A NG H++LSL + T + Sbjct: 193 ALGVAAADRAVNLREITREIARQMGLDLSFAPKTSEQAVCNGVHLHLSLQDLTGHPVMYD 252 Query: 259 TDSDRALSSTGRHFVGGVLAHLPALLALTSPTVNSYARLQPQSGAAAFGCWGIGNREAAI 318 + LS+ G+H+ GVL +LPAL A T+PT SY RLQP +A++ C G NREAA+ Sbjct: 253 AGTSNGLSTLGQHWAAGVLHYLPALCAFTAPTPVSYERLQPHHWSASYACLGQRNREAAL 312 Query: 319 RV-PEVPTNKRETATR--IEFRPADNTANPYLSLLGLLAAGWDGVQNEIDPGRPLDEDPG 375 R+ P V + A + +EFR D TA+P+L++ LL AG G++ + DE P Sbjct: 313 RICPTVSLGGKAVAAQYNLEFRAMDATASPHLAMAALLIAGRLGIEQRLALNAITDEVPD 372 Query: 376 NCSDELLDERGIERLPQTLGEALDALEKNEVLREALGEQLFDSYLTVKRHE 426 + ++E RGI LP +L +AL L +E L EAL L D++ +K E Sbjct: 373 SLNEEQRQARGIVALPASLSQALKCLRNSEALIEALPSALLDTWFALKTEE 423 Lambda K H 0.317 0.134 0.402 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: 446 Number of extensions: 18 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: 446 Length of database: 443 Length adjustment: 32 Effective length of query: 414 Effective length of database: 411 Effective search space: 170154 Effective search space used: 170154 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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