Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5210164 Shew_2608 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__PV4:5210164 Length = 357 Score = 159 bits (401), Expect = 1e-43 Identities = 102/332 (30%), Positives = 173/332 (52%), Gaps = 41/332 (12%) Query: 19 PLILQS-FGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASP 77 PL+L F +++I+ L + ALGLNI+VG+ G + LG+ AF+ GA+ AS Sbjct: 43 PLVLDGYFLTLFIQISYLGIA----ALGLNILVGFTGQISLGHGAFFGFGAF-----ASA 93 Query: 78 HLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGE 137 L +F + + IP+A L G M G P +++G YLAI TL Sbjct: 94 WLNTSF-----------NIPVVFCIPLAGFLTMGVGMMFGMPAARIKGLYLAIATLAAQF 142 Query: 138 IIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLV 197 II+ F + + G G + + +FGFD ++ +Y++ L + Sbjct: 143 IIQDFFGRAEW---FSGGSSGA------------MAAPVSLFGFDFDTDMSFYFIALFAL 187 Query: 198 VVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGA 257 V I L SR GRA++A+R+ ++A+ MG+ +LL+FG+ + + G+ GA++ Sbjct: 188 VFMYIWGCNLMRSRDGRAFVAVRDHYLSAEIMGVKLNKYRLLSFGISSFYAGIGGALYAH 247 Query: 258 FQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDG 317 + G+VS E F+++ S+ +AMV++GG+G I G ++G V + LPEVL + G ++ G Sbjct: 248 YLGYVSSEGFTILMSIQFLAMVIIGGLGSIKGTLMGVVFMVLLPEVLEGMVGLMKYTDYG 307 Query: 318 RLDS-----AILRQLLIALAMIIIMLLRPRGL 344 L A ++++ I L +I+ ++ P GL Sbjct: 308 NLPMVTDGLAYIKEMAIGLVIILFLIFEPEGL 339 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: 311 Number of extensions: 19 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: 357 Length adjustment: 29 Effective length of query: 329 Effective length of database: 328 Effective search space: 107912 Effective search space used: 107912 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: 49 (23.5 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