Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS00890 HSERO_RS00890 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS00890 Length = 404 Score = 459 bits (1181), Expect = e-134 Identities = 228/360 (63%), Positives = 281/360 (78%), Gaps = 24/360 (6%) Query: 15 LLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALM 74 ++V P + Q FGN+WVRI D+ALLY++LALGLN+VVG+AGLLDLGY+AFYA+GAY L+ Sbjct: 26 MIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLDLGYIAFYAIGAYSAGLL 85 Query: 75 ASPHLADNFAAFAAMFP----------------NGLHTSLWIVIPVAALLAAFFGAMLGA 118 ASP A +F +P NG+H SLW+++P++A LAA FGA+LGA Sbjct: 86 ASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISAFLAALFGALLGA 145 Query: 119 PTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDL------ 172 PTLKLRGDYLAIVTLGFGEIIRIF+NNL+ PVN+TNGP+G+ ID +KVFG+ L Sbjct: 146 PTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVFGVSLAGEPGS 205 Query: 173 GKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGIN 232 G ++VFG + SV YY+LFL+L + + RLQDSR+GRAW+AIREDEIAAKAMGIN Sbjct: 206 GSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLGRAWVAIREDEIAAKAMGIN 265 Query: 233 TRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVIL 292 TRN+KLLAF MGASFGGV+GAMFGAFQGFVSPESFSL ES+ ++AMVVLGGIGHIPGV+L Sbjct: 266 TRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMVVLGGIGHIPGVVL 325 Query: 293 GAVLLSALPEVLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEH 350 G V+L+ALPEVLR+V P+Q G+ +D+ +LRQLL LAM++IML RP GLWPSP H Sbjct: 326 GGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLAMVVIMLTRPAGLWPSPRH 385 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: 507 Number of extensions: 18 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: 358 Length of database: 404 Length adjustment: 30 Effective length of query: 328 Effective length of database: 374 Effective search space: 122672 Effective search space used: 122672 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: 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