Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS08920 Length = 655 Score = 165 bits (418), Expect = 3e-45 Identities = 100/329 (30%), Positives = 179/329 (54%), Gaps = 48/329 (14%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68 ++G VAL +P+++ + ++ + + L+Y +L GL+IVVGY G + LG+ + +G+ Sbjct: 10 LLGIVALAGIPMVVHN--PYYLHLIETILIYAILLFGLDIVVGYTGQVSLGHAGLFGIGS 67 Query: 69 YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128 Y AA F G+ +++ +P A + A FGA+L P L++ G YL Sbjct: 68 Y--------------AAGVLFFKLGM--PIFVTVPAAIAVTAVFGAILALPALRVTGPYL 111 Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTL 188 A+VTL FG II+I +N + LT GP G+ L K + G D S Sbjct: 112 AMVTLAFGTIIQILINEMTF---LTEGP-----------LGIKLQKPM--IGGDKMSEVQ 155 Query: 189 YYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFG 248 ++YL VL+V+S+++ +R+ S +GRA+ A+R+ IA+ MG++ K+ AF + A+ Sbjct: 156 FFYLVAVLMVLSMLVVHRILKSNLGRAFQALRDSPIASDCMGVSVYRYKVYAFIISAALA 215 Query: 249 GVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVA 308 G+SGA++ + ++SP +++ ++M + V++GG G ++GA+++ LP +L Sbjct: 216 GLSGALYAYSEEYISPNTYNFELTIMFLLAVIMGGRKSRIGSLIGALIVVMLPSLLS--- 272 Query: 309 GPLQAMTDGRLDSAILRQLLIALAMIIIM 337 D A+ RQ+ LA+I+++ Sbjct: 273 -----------DIALFRQIATVLAVIVVV 290 Lambda K H 0.328 0.144 0.430 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: 461 Number of extensions: 18 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: 358 Length of database: 655 Length adjustment: 34 Effective length of query: 324 Effective length of database: 621 Effective search space: 201204 Effective search space used: 201204 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