Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate 201602 SO2458 transporter, putative (NCBI ptt file)
Query= TCDB::Q9A612 (541 letters) >FitnessBrowser__MR1:201602 Length = 529 Score = 571 bits (1472), Expect = e-167 Identities = 294/509 (57%), Positives = 360/509 (70%), Gaps = 21/509 (4%) Query: 44 LSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLVQPIIG 103 L+F QI+NMCFGF GIQ GF LQNAN SRIFQ+LG ++ + ILWIAAP TGLLVQPIIG Sbjct: 29 LNFWQIFNMCFGFLGIQFGFALQNANVSRIFQTLGASIDEIPILWIAAPLTGLLVQPIIG 88 Query: 104 HFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITMEPFRA 163 + SD TWG GRRRPYF GAILTTLA+ VMP+SPTLW+AA LWIMDASINI MEPFRA Sbjct: 89 YLSDNTWGCLGRRRPYFLIGAILTTLAIFVMPHSPTLWIAAGMLWIMDASINIAMEPFRA 148 Query: 164 FVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSVRIAFY 223 FVGDNLP QR GYAMQSFFIG+GAV ASALP++L+N+F+VANTAPAG++ DSVR AFY Sbjct: 149 FVGDNLPPSQRTQGYAMQSFFIGIGAVVASALPYILSNFFNVANTAPAGEIADSVRYAFY 208 Query: 224 TGGAGLLLAVLWTVFTTREYSPEQLTAFE---KAEREIAGLGLHEEPEPSVNAYIALGVG 280 GG L LAV WTV +T+EYSPE+L AF K + E + +++ +G Sbjct: 209 FGGTVLFLAVTWTVISTKEYSPEELAAFHAKTKTDVEEQCKRSRTHKDYQFASFVWMG-- 266 Query: 281 GVLLGAALALIVWGAGLEKELYVLAGLLFAFG---------LAGVAGARFKRIGRTDNGF 331 LGA L VW L+K+LY+L+ +FAFG L+ ++ ++G N Sbjct: 267 ---LGALLTFTVWAQDLDKQLYILSIGIFAFGPLQLYCALRLSQSQPSQRAQLGMVFN-- 321 Query: 332 SEVLADVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADW 391 V+ D+F MPK M QLA+VQFFSWF LFAMWIYTT AV + HFG+ D S+AYN+GADW Sbjct: 322 --VVDDLFHMPKAMHQLAIVQFFSWFALFAMWIYTTSAVTSYHFGSSDVLSQAYNDGADW 379 Query: 392 VGVLFAVYNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMV 451 VGVLFA YNG +A+AAL IPL+ K +++H + G GL+SF I+DP LLW+ M+ Sbjct: 380 VGVLFASYNGFSAIAALFIPLLAKRIGIKLTHTFNMFCGGFGLISFYFIKDPNLLWLAMI 439 Query: 452 GVGFAWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQS 511 GVG AW+SILS PY+IL+G LP +KMGVYMGIFN FIV+PQLLAA++LGL+L F Q Sbjct: 440 GVGIAWASILSIPYAILSGTLPPKKMGVYMGIFNFFIVIPQLLAASVLGLILNGLFDGQP 499 Query: 512 IFALVLGALSFALAAAATFLVRDRVAGAP 540 I+AL+ G + A A V A P Sbjct: 500 IYALITGGVFMLCAGIAVLFVEQPKALTP 528 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: 847 Number of extensions: 33 Number of successful extensions: 2 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: 529 Length adjustment: 35 Effective length of query: 506 Effective length of database: 494 Effective search space: 249964 Effective search space used: 249964 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