Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate SMc01594 SMc01594 hypothetical protein
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Smeli:SMc01594 Length = 454 Score = 174 bits (441), Expect = 5e-48 Identities = 121/378 (32%), Positives = 178/378 (47%), Gaps = 22/378 (5%) Query: 71 DMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDG-TPVAISPRRVLRRVLELYKAKGWKPV 129 D PD ST+R IPW ++ TA V+ D + D V SPR +L++ + +A G+K Sbjct: 79 DYTMKPDLSTLRRIPW-LEGTALVLCDMLDHDTHAEVPHSPRAILKKQVARLEAMGFKAY 137 Query: 130 IAPELEFYLVDMNKDP-------DLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIY 182 +A ELEF+L D + D DL L + Y I + + + I Sbjct: 138 MASELEFFLFDQSYDDARLSGYRDLQLASGYN---------EDYHIFQTTKEEDVMRAIR 188 Query: 183 EYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMA 242 + + V+ E A Q EIN + D L +AD + K +E A + TF+A Sbjct: 189 NGLQGAGIPVENSKGEASAGQEEINVRYADALTMADRHAIIKNGCKEIAWQRGKAITFLA 248 Query: 243 KPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK--PTSLFTSYIAGLQKYTPALMPIFAP 300 K GS+ H+HQSL ++ LF +G+ + L Y+AG + + AP Sbjct: 249 KWNYSAAGSSSHIHQSLWSKDGETPLFFDKNGQYGMSELMRHYVAGQLAHASEVTYFLAP 308 Query: 301 YINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATL 360 YINSY+R AP W DNRT G+R+ G A RIE R+ G D NPYLA AA + Sbjct: 309 YINSYKRFMAGTFAPTKAIWSKDNRTAGYRLCGEGSKAIRIECRVGGSDLNPYLAFAALI 368 Query: 361 AAGYLGMTQKLEATEPLLSDGYE--LPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYL 418 AAG G+ K+E P + D Y+ ++P L E + + + GE+ V Y+ Sbjct: 369 AAGIAGIENKMELEAPFVGDAYQGKEVREIPHTLREAGEALSGSKMLRAAFGEEVVDHYV 428 Query: 419 ALKETEYEAFFRVISSWE 436 E E + + R ++ WE Sbjct: 429 HAAEWEQQEYDRRVTDWE 446 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: 482 Number of extensions: 21 Number of successful extensions: 5 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: 454 Length adjustment: 33 Effective length of query: 411 Effective length of database: 421 Effective search space: 173031 Effective search space used: 173031 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