Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Synpcc7942_2296 Synpcc7942_2296 L-glutamine synthetase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4509 (423 letters) >FitnessBrowser__SynE:Synpcc7942_2296 Length = 434 Score = 148 bits (373), Expect = 4e-40 Identities = 119/392 (30%), Positives = 178/392 (45%), Gaps = 35/392 (8%) Query: 41 LGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQVVTKFD 100 L L DAD + P D+L PWQ P + L +P PR VL++V++ + Sbjct: 54 LDLSPADADVLAIPDRDSLFQLPWQ--PEVAWMPADLYLNDQPLEQAPRWVLKRVLSVAE 111 Query: 101 ELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQ-VYLIDDLDEYVDCLQDI 159 LG E EF+L+D+ I+ R + Y L D + I Sbjct: 112 SLGYRPKTGVECEFFLLDETG---------DAIADPRDRQAKPCYDQQSLMRRYDLITQI 162 Query: 160 LEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTF 219 E +E G E A QFE+N + AD + D K ++K +A + TF Sbjct: 163 SEAMEELGWGPYQSDHEDANGQFEMNWTY-ADALVTADRQAFFKYMVKTLAERQGLRATF 221 Query: 220 MAKPYPGQAGNGLHVHISILDKDG-KNIFASEDPEQNAALR----HAIGGVLETLPAQMA 274 M KP+ GNG H+H+S+ +++G N F DP A L IGG+L + + A Sbjct: 222 MPKPFADLTGNGCHMHLSLWNREGTTNTFV--DPVATAPLSTLGYQFIGGLLHSAASLCA 279 Query: 275 FLCPNVNSYRRFGA------QFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADA 328 P +NSY+R A + PN ++ +NRT +R+P DA R E R+A A Sbjct: 280 LTNPTINSYKRINAPATTSGATWSPNGISYSGNNRTHLIRIP----DAGRFELRLADGAA 335 Query: 329 NPYLLMASVLAGVHHGLVNKIEPGAPVEGNSYEQ-----NEQSLPNNLRDALRELDDSEV 383 NPYLL A+ +A G+ NK +PG + ++Y Q +LP +L DALR L +S V Sbjct: 336 NPYLLPAAAIAAGLDGIQNKRDPGPRYDNDNYAQPLPPGTVPTLPEHLLDALRSLQESTV 395 Query: 384 MAKYIDPKYIDIFVACKESELEEFEHSISDLE 415 + + + + ++ K E F I+ E Sbjct: 396 LTEGLGAAFTSAYLKLKHQEWRSFCAEITPWE 427 Lambda K H 0.318 0.137 0.409 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: 455 Number of extensions: 22 Number of successful extensions: 7 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: 423 Length of database: 434 Length adjustment: 32 Effective length of query: 391 Effective length of database: 402 Effective search space: 157182 Effective search space used: 157182 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 17 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