Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate HSERO_RS14695 HSERO_RS14695 ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__HerbieS:HSERO_RS14695 Length = 293 Score = 189 bits (480), Expect = 7e-53 Identities = 113/307 (36%), Positives = 186/307 (60%), Gaps = 20/307 (6%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65 QQ+IN L LGS+YAL ALG+T+V+GVL +IN +HG I M+G+ L L V+Q+A LP Sbjct: 4 QQLINALSLGSVYALFALGFTLVFGVLGVINLSHGAIFMLGSYAALLL---VEQMA--LP 58 Query: 66 GIVQLVIAIVGAIPVCIVVSLLIERIAYRPLR--NAPRLAPLITAIGVSILLQTLAMMIW 123 V L++A+V ++ L+I+ + +PLR NAP L P+I IGV+I++ ++ ++ Sbjct: 59 LWVALLLAMVATG----LLGLIIDVLVLKPLRKRNAPHLIPMIATIGVAIMITNISQGLF 114 Query: 124 GRSPLPFPQ-VMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAE 182 G FPQ +P + V + I+ Q+ ++ +A + MV L+ ++ KT++GRA+RA AE Sbjct: 115 GAENKRFPQGTIPEESVSLGNLHITAVQVAIIVIAFVLMVVLLGVMRKTQLGRALRAIAE 174 Query: 183 NPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLG 242 +P+ A L+G++ + ++T A L AGV+ +++ MG K + +LG Sbjct: 175 SPKAAYLLGINVEGLFLLTSFAAAALGGAAGVLVGVSFNAISPFMGQPMLHKGIAVIILG 234 Query: 243 GIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIMG 302 G+G+I GAM+GG+ LG E L YI S+++D AF +L ++L ++PSG+ G Sbjct: 235 GMGDIRGAMIGGLFLGFAEVLTVAYI--------SSDFRDAVAFGLLFLILLVKPSGMFG 286 Query: 303 ERVADRA 309 + + +A Sbjct: 287 KVLERKA 293 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: 241 Number of extensions: 13 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: 309 Length of database: 293 Length adjustment: 27 Effective length of query: 282 Effective length of database: 266 Effective search space: 75012 Effective search space used: 75012 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