Align Monocarboxylate transport permease protein (characterized)
to candidate BPHYT_RS22245 BPHYT_RS22245 sodium:solute symporter
Query= SwissProt::Q1M7A2 (491 letters) >FitnessBrowser__BFirm:BPHYT_RS22245 Length = 493 Score = 623 bits (1607), Expect = 0.0 Identities = 315/488 (64%), Positives = 375/488 (76%), Gaps = 2/488 (0%) Query: 5 INGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGGDFYT 64 +N A+ VFI FFVLVTV+GF A+RW++ + L + EWGLGGR FGT I+WFLVGGDFYT Sbjct: 7 VNPVAMTVFIAFFVLVTVIGFFAARWKRGD-LTQLHEWGLGGRQFGTVISWFLVGGDFYT 65 Query: 65 AYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVHGQYG 124 AYTVIAVPALVY+VGAYGFFALPYTI+VYPFVF VMP LWK A ++TA D V G+YG Sbjct: 66 AYTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKIAHAKNHITAADYVQGEYG 125 Query: 125 SRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLHGELPLAIAFIVLALYTYSAGLRA 184 + AVA TG++ATMPYIALQLVGM V+K LG+ GE+PL +AF++LALYTY++GLRA Sbjct: 126 GKWFPAAVAITGIVATMPYIALQLVGMQVVIKGLGVTGEMPLIVAFVILALYTYASGLRA 185 Query: 185 PALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQAKGSGN-LLLGGNQYVAY 243 PA+IAFVKDIMIYIVVIAAV LIP+KLGGYA+VF +AD F+AKG ++L Q+ AY Sbjct: 186 PAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDAADTYFKAKGGATGIILKPTQFTAY 245 Query: 244 ATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYMGHAANLK 303 A+LALGSALAAFMYPHT+T + +S+S T+RKNAI LPAYTLLLGL+ALLGYM AA + Sbjct: 246 ASLALGSALAAFMYPHTMTAVLSSSSANTVRKNAIFLPAYTLLLGLIALLGYMAIAAGVH 305 Query: 304 LDSANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVDPDV 363 + SA+D+VP LF TLF WF GFA AAIAI ALVPAA+MSIGAANLFTRN W+ V P++ Sbjct: 306 VKSASDMVPALFNTLFPSWFVGFAAAAIAISALVPAAIMSIGAANLFTRNLWRPLVSPNI 365 Query: 364 SDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWILQTLPALVFGLYTNWFR 423 S GEA AKI SLVVK GALL I+FLPTQ+A+DLQLLGG+WILQ PA+VF LYT Sbjct: 366 SPEGEASTAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWILQIFPAIVFSLYTRRLN 425 Query: 424 APGLLAGWFVGFGGGTFLVWDAGWKPLHLISLGGEPFTVYTGLLALAANIAVAVVVNALL 483 PGL GW G GT L G KP+ + LG + VY GL+AL NI V+ VV+ L Sbjct: 426 TPGLFLGWLAGIVLGTGLAISQGLKPVFALHLGDAVYPVYIGLIALTVNIVVSFVVSVLS 485 Query: 484 PAKAPVRA 491 P + A Sbjct: 486 PRRVVAAA 493 Lambda K H 0.327 0.142 0.439 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: 834 Number of extensions: 50 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: 491 Length of database: 493 Length adjustment: 34 Effective length of query: 457 Effective length of database: 459 Effective search space: 209763 Effective search space used: 209763 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