Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_106714457.1 CU102_RS29025 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_003010955.1:WP_106714457.1 Length = 456 Score = 401 bits (1030), Expect = e-116 Identities = 220/448 (49%), Positives = 283/448 (63%), Gaps = 5/448 (1%) Query: 13 ELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTV 72 EL+R V G++DTV+ F DMQGRL GKR +FV+ A C+YLLA D+D+ V Sbjct: 9 ELKRRVNNGEIDTVLACFVDMQGRLIGKRFHATYFVES-AHDETHGCNYLLANDIDMEPV 67 Query: 73 PGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSE-VAVSPRSILRRQ 131 PGY ASW GYGD ++ PDLST+R IPWL ALV+ D++ E +A SPRSIL+RQ Sbjct: 68 PGYKAASWKQGYGDFIIKPDLSTIRHIPWLEKCALVLCDILDHHHHEDLAHSPRSILKRQ 127 Query: 132 LDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLR 191 L RLK RG +A A+ELEF +FD+ Y A A ++G+ AS Y DY I +++ + ++R Sbjct: 128 LARLKERGYLAYFASELEFYLFDETYETARAKHWKGMNTASPYIQDYVIQMTTKEDAVMR 187 Query: 192 DIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLT 251 IR G+ AG+ E KGE GQ+EI RY EAL D H + KNG KEIA Q GK++T Sbjct: 188 AIRNGLFDAGIPVENSKGEWGPGQEEINVRYAEALEMADRHVVMKNGCKEIATQMGKAIT 247 Query: 252 FMAKYD-EREGNSCHIHVSLRGTDG-SAVFADSNGPHGMSSMFRSFVAGQLATLREFTLC 309 FMAKYD G+S H+H SL DG + +F D H MS + R +VAGQL +FT Sbjct: 248 FMAKYDYSLAGSSSHVHNSLWSADGKTPLFYDKKAEHTMSPLMRQWVAGQLKYADDFTYF 307 Query: 310 YAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHG-QNIRVECRVPGGDVNQYLAVA 368 AP INSYKRF +FAPT W LDNRT R+ G G + IR+ECR+ G D+N YLA A Sbjct: 308 LAPYINSYKRFQAGTFAPTKSVWSLDNRTAGFRLCGEGTKGIRIECRIGGADLNPYLAFA 367 Query: 369 ALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGEDVVA 428 LIA GL GI+ L L P G+AY G ++ +P TL +A S +++EA GEDVV Sbjct: 368 GLIASGLAGIDEKLDLGPPFQGDAYGGTRLKEIPKTLREATETLARSKMLKEALGEDVVE 427 Query: 429 HYLNNARVELAAFNAAVTDWERIRGFER 456 HY++ A+ E ++ VTDWE RGFER Sbjct: 428 HYVHTAKWEQFEYDRRVTDWELHRGFER 455 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: 579 Number of extensions: 27 Number of successful extensions: 6 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: 456 Length adjustment: 33 Effective length of query: 424 Effective length of database: 423 Effective search space: 179352 Effective search space used: 179352 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 Jul 26 2024. The underlying query database was built on Jul 25 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