Align ABC transporter (characterized, see rationale)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 340 bits (873), Expect = 3e-98 Identities = 187/373 (50%), Positives = 245/373 (65%), Gaps = 17/373 (4%) Query: 1 MIKLKLDNVNKQLG-GMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 M + L V K G G ++RDV LEI EF VF+GPSGCGKSTLLR+IAGL+ + GD Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119 L I G+ +ND+ +RGV MVFQSYAL+PHMSV++N++FGLKLAKT K + +V + A+ Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179 ILQL+ LL+RKPK LSGGQRQRVA+GRA+ REP + LFDEPLSNLDA+LR Q R EIARL Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HDRLG-STMIYVTHDQVEAMTLADKIVVLNGGR-------VEQVGSPRELYERPASRFVA 231 H + ++++YVTHDQ+EAMTLADKIV+L+ G+ + Q+G+P ELY RP SRFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 232 GFLGSPRMNFLSARLQTPGETSLVDTL--VWGITSLPFDSSNLAAGTPLSLGIRPEHV-- 287 GF+GSPRMNFL R+ + + TL +P + + L ++LG+RPEH+ Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 288 ----SLKAADGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLD 343 S+ D V+ VE LG +YVHL+ L+ + + G+R L + Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGERASLRVP 360 Query: 344 LDNLHLFDADGVA 356 HLF DG A Sbjct: 361 RAACHLFTEDGFA 373 Lambda K H 0.320 0.137 0.394 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: 372 Number of extensions: 10 Number of successful extensions: 5 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: 381 Length of database: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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