Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 8501367 DvMF_2099 glutamine synthetase, type I (RefSeq)
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Miya:8501367 Length = 447 Score = 176 bits (446), Expect = 1e-48 Identities = 127/393 (32%), Positives = 194/393 (49%), Gaps = 30/393 (7%) Query: 65 TGVTDPDMVCVPDASTIRMIPWAV--DPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYK 122 T + + DMV PDA+T ++ W P A++ D + DGTP PR +LR++ E Sbjct: 66 TRIEESDMVAFPDATTFQICAWRPMERPVARMFCDVRNPDGTPYEGDPRYILRKLTEKAA 125 Query: 123 AKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIY 182 KG+ + PELEF+L ++ P PI G + ++ + + DI Sbjct: 126 QKGYTYYVGPELEFFLFASSQCPQ-----PIDAGGY-------FDAPPLDLGNDVRRDII 173 Query: 183 EYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMA 242 + + V+ HEV +Q EI+ + + +K+AD V +K V+E A +H +YATFM Sbjct: 174 FALQRMGIPVEYSHHEVAPSQHEIDLRYNEAMKMADVVMTYKVVVKEMARKHGVYATFMP 233 Query: 243 KPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKP--TSLFTSYIAGLQKYTPALMPIFAP 300 KP+ G+ GS MH+HQSL G N F P+ + SYIAGL K+ + Sbjct: 234 KPIFGQNGSGMHVHQSLF--RNGRNAFFDPNDPHHLSGECRSYIAGLLKHAREFCCVTNQ 291 Query: 301 YINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGP---AARRIENRIPGVDCNPYLAIA 357 +INSY+RL AP+ +AW NR+ R+P P AA RIE R P CNPYLA + Sbjct: 292 WINSYKRLVPGYEAPVYLAWAQRNRSALIRVPMYKPGKEAATRIELRSPDPACNPYLAFS 351 Query: 358 ATLAAGYLGMTQKLEATEPLLSDGYELPYQ---------LPRNLEEGLTLMGACEPIAEV 408 LAAG G+ + E + + ++ + + + LP +L E + + EV Sbjct: 352 VMLAAGLEGIEKSYELPKAVEANIFHMGEEDLTKHGIGSLPGSLYEAAMELKGSALMQEV 411 Query: 409 LGEKFVKAYLALKETEYEAFFRVISSWERRHLL 441 LGE + K E++A+ +S +E + L Sbjct: 412 LGEHTHANLVGNKLIEWDAYRTHVSEFELQRYL 444 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: 529 Number of extensions: 24 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: 444 Length of database: 447 Length adjustment: 32 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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