Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate N515DRAFT_3387 N515DRAFT_3387 maltose/moltooligosaccharide transporter
Query= TCDB::Q9A612 (541 letters) >FitnessBrowser__Dyella79:N515DRAFT_3387 Length = 497 Score = 544 bits (1402), Expect = e-159 Identities = 286/493 (58%), Positives = 348/493 (70%), Gaps = 17/493 (3%) Query: 44 LSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLVQPIIG 103 L+F QIWNMCFGF GIQ GF LQNAN SRIFQ+LG DV + +LW+AAP +GL+VQPI+G Sbjct: 12 LTFWQIWNMCFGFLGIQFGFALQNANVSRIFQTLGADVGDIPMLWVAAPLSGLIVQPIVG 71 Query: 104 HFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITMEPFRA 163 + SD+TW GRRRPYF GA+L TL LL MPN+P LWVAA LWI+DASIN++MEPFRA Sbjct: 72 YLSDRTWTGLGRRRPYFLVGAVLATLGLLWMPNAPALWVAAGLLWILDASINVSMEPFRA 131 Query: 164 FVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSVRIAFY 223 FVGD LP QR GYAMQSFFIGLGAV ASALPW+L V+N +PD+VR AFY Sbjct: 132 FVGDQLPPRQRPLGYAMQSFFIGLGAVVASALPWILER-LGVSNAPGVSGIPDTVRYAFY 190 Query: 224 TGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALGVGGVL 283 GGA LL +VLWTV +TREY PE L AF+ A E + P+ + + G+ + Sbjct: 191 AGGAVLLGSVLWTVCSTREYPPETLAAFDHAPVEETAVD-----RPAASRW---GLLWLA 242 Query: 284 LGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNG--FSEVLADVFRM 341 G AL +V LEKELY+L G + FG+A +GRT + ++VL D+F M Sbjct: 243 AGLALTAVVAFMRLEKELYLLTGGMSVFGVA------LLWLGRTASRGPAAQVLGDLFGM 296 Query: 342 PKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAVYNG 401 P+ MR+LA VQ FSWF LFAMWIYTT V VH+G+ D S AYNEGA+WVGVLFA YNG Sbjct: 297 PEAMRRLAWVQLFSWFALFAMWIYTTAGVTQVHYGSSDPHSAAYNEGANWVGVLFAAYNG 356 Query: 402 VAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWSSIL 461 AALAA+VIP MV+ R+SH V + LG G LSFL+I DP L + MVGVGFAW+SIL Sbjct: 357 FAALAAIVIPWMVRRWGIRISHLVNVWLGGAGFLSFLLIHDPRWLLLSMVGVGFAWASIL 416 Query: 462 STPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLGALS 521 S PY++L+ LPA KMGVYMGIFN F+V+PQLLAA++LGL+L+ FF Q I+ALVLG S Sbjct: 417 SLPYALLSDNLPAHKMGVYMGIFNFFVVIPQLLAASVLGLLLRAFFHGQPIYALVLGGAS 476 Query: 522 FALAAAATFLVRD 534 ++ VR+ Sbjct: 477 LFVSGLCVLRVRE 489 Lambda K H 0.327 0.140 0.437 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: 934 Number of extensions: 53 Number of successful extensions: 4 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: 541 Length of database: 497 Length adjustment: 35 Effective length of query: 506 Effective length of database: 462 Effective search space: 233772 Effective search space used: 233772 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 (21.7 bits) S2: 52 (24.6 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