Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate 3608585 Dshi_1979 inner-membrane translocator (RefSeq)
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__Dino:3608585 Length = 305 Score = 147 bits (370), Expect = 4e-40 Identities = 95/314 (30%), Positives = 170/314 (54%), Gaps = 29/314 (9%) Query: 5 IQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGL-------SLLKVV 57 IQ +++G+++G++ +L A+G T+ +L NF+H ++L +GA L +LL + Sbjct: 2 IQHLLDGILVGAILSLGAIGLTLTMHMLRFANFSHAELLSIGAYAALVFDALFSALLPAL 61 Query: 58 QQVAPGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRN-APRLAPLITAIGVSILLQ 116 Q P L L +A V ++ + + ++ I+R+ ++ +R L+ + + GV+++++ Sbjct: 62 QTAIPPLSLTWTLSLATVASMALTGLSAIAIDRLIFKRVREKGGELSMVFASFGVAMVIR 121 Query: 117 TLAMMIWGRSP------LPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEK 170 L + +G + + F V+ DP+ L+ P Q+ L A+ MV L L++ + Sbjct: 122 NLIGLGFGLNTQLYSDDIVFATVLSRDPL----ILVKPDQVFTLVAALAIMVVLHLVLSR 177 Query: 171 TKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWA-ANYSTAQFAMGF 229 T G ++RA AENP +A + G++ +++ + + +G LAA AGV + N T Sbjct: 178 TTFGYSLRAVAENPVLAQVSGINLQRMVALIWILGGTLAAAAGVFYGLTNQITPVIGRDL 237 Query: 230 VPGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVL 289 V L F+A ++GGIG+IYGA+LGG L+G+ +L L S Y F++L Sbjct: 238 V--LPIFAATIVGGIGSIYGAVLGGFLVGIAANLAL--------VVLPSGYSPSVPFLIL 287 Query: 290 IIVLTLRPSGIMGE 303 + VL LRP G+ GE Sbjct: 288 VAVLVLRPHGLFGE 301 Lambda K H 0.328 0.144 0.416 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: 209 Number of extensions: 10 Number of successful extensions: 4 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: 309 Length of database: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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: 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