Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012406807.1 BPHY_RS38400 glutamine synthetase family protein
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_000020045.1:WP_012406807.1 Length = 452 Score = 414 bits (1063), Expect = e-120 Identities = 216/450 (48%), Positives = 288/450 (64%), Gaps = 3/450 (0%) Query: 9 LAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVD 68 L + L++ VA+G +DTV+V DMQGRL GKR G FV C+YLLA D++ Sbjct: 3 LRFDALKQAVASGVIDTVLVCMVDMQGRLIGKRFHGDFFVKS-GYLETHACNYLLANDME 61 Query: 69 LNTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVSPRSIL 128 + V GYA ASW GYGD V+ PDLSTLR +PWL GTALVI D++ G VA SPR IL Sbjct: 62 MEPVAGYASASWAEGYGDFVLKPDLSTLRRLPWLEGTALVICDVLDQSGQPVAHSPRQIL 121 Query: 129 RRQLDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEP 188 ++QL RL RG+ A A+ELEF +F++ Y + YR LT Y+ DY IL+++R E Sbjct: 122 QKQLSRLTERGMSACFASELEFYLFNETYEETSVKKYRDLTTCGTYSHDYHILSTTRQES 181 Query: 189 LLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGK 248 ++R IR G+ AG+ E KGE GQ EI Y + L+ D H + K+G+KEIA Q K Sbjct: 182 VMRPIRNGLHEAGIAIECSKGEWGAGQGEINVHYADPLMMADQHTMIKHGSKEIASQQKK 241 Query: 249 SLTFMAKYD-EREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFT 307 ++T+MAK++ G+SCHIH SL DG+ +F + + P+GMS++ RS++AG L R+ T Sbjct: 242 AITYMAKWNYGLPGSSCHIHSSLWTLDGTPLFLEKSSPYGMSNLMRSYLAGLLRYSRDIT 301 Query: 308 LCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN-IRVECRVPGGDVNQYLA 366 L AP +NSYKRF SFAPT W LDNRT RV G G + +RVECR+ G D+N YLA Sbjct: 302 LFLAPYVNSYKRFQKGSFAPTRTVWSLDNRTAGFRVCGEGSHAVRVECRIGGADLNPYLA 361 Query: 367 VAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDV 426 A LIA GL GI+ L+LP P +G+AY ++ +P TL +A DS L+RE FG+ V Sbjct: 362 FAGLIAAGLAGIDHKLELPGPLIGDAYLDGELPEIPKTLREAITAASDSTLLREVFGDTV 421 Query: 427 VAHYLNNARVELAAFNAAVTDWERIRGFER 456 HY++ A+ E ++ +TDWE RGFER Sbjct: 422 TNHYVHAAQWEQLEYDRRITDWELTRGFER 451 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: 585 Number of extensions: 29 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: 457 Length of database: 452 Length adjustment: 33 Effective length of query: 424 Effective length of database: 419 Effective search space: 177656 Effective search space used: 177656 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 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