Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Synpcc7942_2156 Synpcc7942_2156 L-glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__SynE:Synpcc7942_2156 Length = 473 Score = 140 bits (354), Expect = 7e-38 Identities = 119/395 (30%), Positives = 186/395 (47%), Gaps = 47/395 (11%) Query: 67 VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFD---GTPVAISPRRVLRRVLELYKA 123 + + DM VPD +T + P+ +PT +I C ++ TP PR + ++ ++ KA Sbjct: 63 INESDMTMVPDPTTAWIDPFMKEPTLSMI--CTIYEPRTNTPYERCPRAIAQKAVDYLKA 120 Query: 124 KGWKPV--IAPELEFYLVD---MNKDPDLPLQPPIGRTGRPETGRQAYSIEAVN-EFDPL 177 G PE EF++ D ++ + GR +GR+ E N + P Sbjct: 121 SGIGDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREE---EGGNLGYKPR 177 Query: 178 FEDIY----EYCEVQELEVDTLI-------------HEVGAA-QMEINFMHGDPLKLADS 219 +++ Y Q++ + L+ HEV Q E+ F G ++ AD Sbjct: 178 YKEGYFPVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADW 237 Query: 220 VFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSL 279 + +K ++ R+ TFM KP+ + GS MH HQS+ ++ G LF G S Sbjct: 238 LMTYKYVIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWND--GQPLFAGDQYAGLSQ 295 Query: 280 FTS-YIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSG--P 336 YI G+ K+ PAL+ + P NSY+RL AP+N+A+ NR+ RIP SG P Sbjct: 296 MALWYIGGILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNP 355 Query: 337 AARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYEL-PYQL------P 389 A+R+E R P NPYLA AA L AG G+ +++ EPL D Y+L P +L P Sbjct: 356 KAKRLEFRCPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTP 415 Query: 390 RNLEEGLTLMGACEPIAEVLG---EKFVKAYLALK 421 +L++ L + A V G E F++ ++ K Sbjct: 416 GSLKDALKALEADHDFLTVGGVFTEDFIQNWIEYK 450 Lambda K H 0.321 0.138 0.418 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: 578 Number of extensions: 30 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 473 Length adjustment: 33 Effective length of query: 411 Effective length of database: 440 Effective search space: 180840 Effective search space used: 180840 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 (21.8 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