Align ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized)
to candidate BWI76_RS17840 BWI76_RS17840 sugar ABC transporter permease
Query= TCDB::Q8NMV4 (281 letters) >FitnessBrowser__Koxy:BWI76_RS17840 Length = 313 Score = 142 bits (358), Expect = 9e-39 Identities = 90/280 (32%), Positives = 144/280 (51%), Gaps = 15/280 (5%) Query: 11 VFVLPTLLAFMIAFLVPFIVGFFLSFTKFTTITNAKWVGIDNYVKAFSQREGFISAFGFT 70 +F+ P L+ F +P I G +SF K +WVG+DN+ +AF+ E +A T Sbjct: 35 LFLAPALIIFSWFKFIPMIQGLVMSFYKVNFNQPNEWVGLDNFTRAFADAE-LHAAVVNT 93 Query: 71 VLVVIVSVITVNIFAFLLAWLLTRKLRGTNFFRTVFFMPNLIGGIVLGYTWQTMIN---- 126 +L V+V++ I AF LA LL R F RT F+P + ++ W+ + N Sbjct: 94 LLYVVVTMFAAAILAFFLAMLLEGPARHLRFIRTAIFLPAVTSAAIVAEMWRILFNPTPN 153 Query: 127 AVLSHYATTIS-ADWKFGYA-----GLIMLLN-WQLIGYMMIIYIAGLQNVPPELIEAAE 179 V++H + AD F + G+IMLL+ W+ + Y M+I+IAGL + +L +AA Sbjct: 154 GVVNHILSWFGVADQGFLASSDQALGVIMLLHIWKAVPYNMVIFIAGLAGISRDLYDAAN 213 Query: 180 LDGVNKWEMLRHVTIPMVMPSITICLFLTLSNSFKLFDQNLALTNGAPGGQTEMVALNII 239 +DG + W LR+VT+P ++P++++ L L+ F++F + A T G P TEMV +I Sbjct: 214 VDGASWWNRLRYVTLPGMIPALSVVLMLSFIRGFRVFAEVYATTGGGPSNATEMVMTHIY 273 Query: 240 NTLFNRMNVEGVGQAKAVIFVVVVVVIAYFQLRATRSKEI 279 F + + G A AV F++ + T K I Sbjct: 274 KLGFEQFD---YGYASAVSFLLFTFTVLLTICHLTLKKRI 310 Lambda K H 0.331 0.142 0.431 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: 239 Number of extensions: 15 Number of successful extensions: 3 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: 281 Length of database: 313 Length adjustment: 26 Effective length of query: 255 Effective length of database: 287 Effective search space: 73185 Effective search space used: 73185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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