Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_090446707.1 BLS63_RS16675 glutamine synthetase
Query= reanno::pseudo5_N2C3_1:AO356_13135 (458 letters) >NCBI__GCF_900100495.1:WP_090446707.1 Length = 459 Score = 837 bits (2163), Expect = 0.0 Identities = 403/459 (87%), Positives = 437/459 (95%), Gaps = 1/459 (0%) Query: 1 MSVPPRAVQLNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPAS 60 MSVP RAVQLNEANAFLKEHPEV +VDLLIADMNGVVRGKRIER SLHKVYEKGINLPAS Sbjct: 1 MSVPLRAVQLNEANAFLKEHPEVQFVDLLIADMNGVVRGKRIERASLHKVYEKGINLPAS 60 Query: 61 LFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFF 120 LFALDINGSTVESTGLGLDIGDADRIC+PIP+TLCNEPWQKRPTAQLLMTMHEL+G+PFF Sbjct: 61 LFALDINGSTVESTGLGLDIGDADRICFPIPNTLCNEPWQKRPTAQLLMTMHELDGKPFF 120 Query: 121 ADPREVLRQVVTKFDELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYL 180 ADPREVLRQV+ KFDELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYL Sbjct: 121 ADPREVLRQVIQKFDELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYL 180 Query: 181 IDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRL 240 IDDLDEYVDCLQD+LE AKEQ +PADAIVKESAPAQFEVNLHH D +KACD+A+LLKRL Sbjct: 181 IDDLDEYVDCLQDMLEAAKEQDLPADAIVKESAPAQFEVNLHHTNDALKACDHALLLKRL 240 Query: 241 IKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILD-KDGKNIFASEDPEQNAALRHAIGG 299 IKNIAYDHEMD+TFMAKPYPGQAGNGLHVHIS+LD K G+NIFA+E+P ++ LRHAIGG Sbjct: 241 IKNIAYDHEMDSTFMAKPYPGQAGNGLHVHISLLDKKTGQNIFATEEPLESEVLRHAIGG 300 Query: 300 VLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVA 359 +LET+PA MAFLCPNVNSYRRFGAQFYVPN+P+WGLDNRTVA+RVPTGSAD+VR+EHRVA Sbjct: 301 ILETMPASMAFLCPNVNSYRRFGAQFYVPNAPSWGLDNRTVAVRVPTGSADSVRIEHRVA 360 Query: 360 GADANPYLLMAAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVM 419 GADANPYL+MAA+LAG+HHG+ NKIEPG P+EGNSYEQ EQSLPNNLRDALRELDDSEV+ Sbjct: 361 GADANPYLMMAAILAGIHHGMTNKIEPGEPIEGNSYEQLEQSLPNNLRDALRELDDSEVL 420 Query: 420 AKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV 458 KYI P YIDIFVACKE+EL+EFE +ISDLEYNWYLHTV Sbjct: 421 NKYISPDYIDIFVACKEAELQEFETTISDLEYNWYLHTV 459 Lambda K H 0.318 0.137 0.408 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: 901 Number of extensions: 20 Number of successful extensions: 2 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: 458 Length of database: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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