Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate WP_008627553.1 C943_RS21420 MFS transporter
Query= TCDB::Q9A612 (541 letters) >NCBI__GCF_000330725.2:WP_008627553.1 Length = 493 Score = 283 bits (725), Expect = 8e-81 Identities = 168/503 (33%), Positives = 259/503 (51%), Gaps = 32/503 (6%) Query: 39 MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98 M + +L+F QI NM GFFGIQ FGLQ + + I+ LG + + IL +A P TGLL+ Sbjct: 1 MQKPQLTFSQIINMNVGFFGIQYSFGLQQSAVNPIYDMLGAQPHEIPILNLAGPMTGLLI 60 Query: 99 QPIIGHFSDKTWG-RFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINIT 157 QPIIG SD+TW RFGRR+P+FF GA+ ++ L + P S TLW+AA LW++DA+ N Sbjct: 61 QPIIGALSDRTWSPRFGRRKPFFFIGAVFCSICLFLYPFSSTLWMAAGLLWVLDAANNTA 120 Query: 158 MEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDS 217 MEP+RA + D LP+EQ ATG+ QSFF GLG A+ + +F + AG +P Sbjct: 121 MEPYRALIADKLPEEQYATGFLTQSFFTGLGITLAN----LSLFFFQMYIPGTAGSLPVW 176 Query: 218 VRIAFYTGGAGLLLAVLWTVFTTREY--SPEQLTAFEKAEREIAGLGLHEEPEPSVNAYI 275 V +F+ G + +V W+++ T E SP++L ++ + P P + ++ Sbjct: 177 VYASFFLGSVCSIASVGWSIYKTSEIPPSPDELQVLKEKNEGM--------PHPVIQFFL 228 Query: 276 ALGVGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFS--- 332 ++ + L L+V +F G+ ++ + FS Sbjct: 229 SVVTSLFIYALFLVLLV-------------PAIFDRGILRRTVHAIEKRPSSKVLFSQNL 275 Query: 333 EVLADVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVA-TVHFGAVDASSKAYNEGADW 391 E+++ + MP M +LA+V F W+ LF W ++A +V + + Y E W Sbjct: 276 EIISAILDMPSVMWKLALVYLFQWYALFVYWQNAAKSIAQSVWNTSPSENMDLYEEAVGW 335 Query: 392 VGVLFAVYNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMV 451 G++ YN V L+A + + K + H CL + LGLL F I + LL+ M Sbjct: 336 TGLVNGWYNVVTFLSAFALVGVAKRFGPKKVHFFCLIVAGLGLLVFPFIENKYLLFAPMT 395 Query: 452 GVGFAWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQS 511 G G AW+S++ PY ++ +P + GVYMGI N+ IVVP + G + K F GN Sbjct: 396 GFGIAWASMMGIPYLLVVNEIPKERYGVYMGIINMMIVVPMIFQTLSFGFVAKNFLGNDP 455 Query: 512 IFALVLGALSFALAAAATFLVRD 534 ++ + LAA A +++ Sbjct: 456 GISIAFAGVLLLLAAVAVLRIKE 478 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: 651 Number of extensions: 38 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 541 Length of database: 493 Length adjustment: 35 Effective length of query: 506 Effective length of database: 458 Effective search space: 231748 Effective search space used: 231748 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 24 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