Align N-acetylglucosamine porter, NagP (characterized)
to candidate Echvi_3909 Echvi_3909 Fucose permease
Query= TCDB::Q8EBL0 (435 letters) >FitnessBrowser__Cola:Echvi_3909 Length = 469 Score = 195 bits (495), Expect = 3e-54 Identities = 146/458 (31%), Positives = 230/458 (50%), Gaps = 59/458 (12%) Query: 14 PMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWV-- 71 P+ +V LFF+ GF T +N L+P+L+Q+ L +QA LI +F+ A F +L + Sbjct: 26 PLFLVTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGAYFFISLGYYLISI 85 Query: 72 -----IRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVN 126 I ++GYKNG+ LG+ + + L F PAA F FLFA V+ +G T+LQ A N Sbjct: 86 TKGDPIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFVLASGITILQIAAN 145 Query: 127 PYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMAN 186 PYV LG A++R+++ N IAPL+ LI + D +D A+ Sbjct: 146 PYVTILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGAIGD----------VDISAD 195 Query: 187 GLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLALF 246 + +PY+ +A+ + ++AL K LPE+ ++ + + AL H +L LG+ A+F Sbjct: 196 SVKMPYVALALTLLLIALIFKLFKLPEIGSQGVIISDS------GALKHRHLMLGIGAIF 249 Query: 247 VYVAVEVIAGDTIGTFAL---SLGID-----HY------GVMTSYTMVC----------- 281 YV EV G + FA G+D HY G M Sbjct: 250 AYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFWGGAMVGRFFGAVALADFKHNLN 309 Query: 282 --MVLGYILGI--LLIPRVISQPTALMISAILGLLLTLGIL--FGDNNS---YAIANLLL 332 +++G I I + I V AL A +GL + + I+ F N + + I + L Sbjct: 310 RFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVVIIIGQFIPNRTLWLFGITGIGL 369 Query: 333 VPFGGVALPD-TLLLIAFLGLANAIVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGP 391 + G + L I LGL N+I++P ++ LA+ G+GK T+ S+LL+M I GGA P Sbjct: 370 LVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGLGKYTAQASSLLVMAIVGGAIVP 429 Query: 392 VSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHKM 429 + GL++ + Q ++V L CYL+I+FY +KG+++ Sbjct: 430 LLQGLLADISG-SVQLSFLVPLACYLYIVFYGMKGYRV 466 Lambda K H 0.326 0.141 0.414 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: 612 Number of extensions: 48 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: 435 Length of database: 469 Length adjustment: 33 Effective length of query: 402 Effective length of database: 436 Effective search space: 175272 Effective search space used: 175272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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