Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate GFF4503 PS417_23050 trehalose permease IIC protein
Query= BRENDA::P12655 (664 letters) >FitnessBrowser__WCS417:GFF4503 Length = 480 Score = 362 bits (929), Expect = e-104 Identities = 193/475 (40%), Positives = 302/475 (63%), Gaps = 14/475 (2%) Query: 2 DYSKVASEVITAVG-KDNLVAAAHCATRLRLVLKDDSKVDQKALDKNADVKGTFKTDGQY 60 DYS +A E++ +G DNL AAHC TRLRL LKD S V+ AL++ VKG+F T G + Sbjct: 4 DYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTGGLF 63 Query: 61 QVIIGPGDVNFVYDEIIKQTGLTEVSTDDLKKIAASGKKFNPIMALIKLLSDIFVPIIPA 120 QV+IGPG+V VY + +QTGL + D+KK A K N + L+++ SD+F+PI+PA Sbjct: 64 QVVIGPGEVEKVYAALREQTGLAAATIADVKKKGAD--KTNAMQRLVRVFSDVFMPILPA 121 Query: 121 LVAGGLLMALNNFLTSEGLF-GTKSLVQQFPIIKGSSDMIQLMSAAPFWFLPILVGISAA 179 L+ GLLM +NN + ++G+F K+L++ +P + G +I LM+ F FLP LVG SAA Sbjct: 122 LIIAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSAA 181 Query: 180 KRFGANQFLGASIGMIMVAPGAANIIGLAANAPISKAATIGAYTGFWNIFG-LHVTQASY 238 KRFG ++ LG +G+++V P N A N + A G +++IFG + + Y Sbjct: 182 KRFGGSEILGIVLGLMLVHPDLLN----AWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGY 237 Query: 239 TYQVIPVLVAVWLLSILEKFFHKRLPSAVDFTFTPLLSVIITGFLTFIVIGPVMKEVSDW 298 Q++P+L+A +++S++EK R+P+A+ P+ ++++TG L +IGPV + + Sbjct: 238 QGQILPILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGIL 297 Query: 299 LTNGIVWLYDTTGFLGMGVFGALYSPVVMTGLHQSFPAIETQLISAFQNGTGHGDFIFVT 358 +T G+V L+D +G +FG LY+P+V+TG+H F A++ QLIS T G FI+ Sbjct: 298 ITEGVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLIS-----TQGGTFIWPM 352 Query: 359 ASMANVAQGAATFAIYFLTKDKKMKGLSSSSGVSALLGITEPALFGVNLKYRFPFFCALI 418 M+N+AQG+A A+++ T++ + K ++S+S +SA GITEPA+FGVNL+++FPF+ AL+ Sbjct: 353 IVMSNLAQGSAALAVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALV 412 Query: 419 GSASAAAIAGLLQVVAVSLGSAGFLGFLSIKASSIPFYVVCELISFAIAFAVTYG 473 GSA + L +V A ++G G GF+SI SI +V+ +I+ + F +T G Sbjct: 413 GSALGSIFLALNKVQASAIGVGGLPGFISIVPQSIAVFVIGMVIAMVVPFVLTCG 467 Lambda K H 0.320 0.135 0.384 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: 680 Number of extensions: 30 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: 664 Length of database: 480 Length adjustment: 36 Effective length of query: 628 Effective length of database: 444 Effective search space: 278832 Effective search space used: 278832 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: 53 (25.0 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