Align RhaQ (characterized, see rationale)
to candidate HSERO_RS22210 HSERO_RS22210 branched-chain amino acid ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__HerbieS:HSERO_RS22210 Length = 339 Score = 338 bits (868), Expect = 9e-98 Identities = 176/330 (53%), Positives = 239/330 (72%), Gaps = 2/330 (0%) Query: 1 MSTVSTQPEKRI-IPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDA 59 M+ ++ P R I ++ R + WE LL + VL+ N L P+F D +NL+D+ Sbjct: 4 MNEPASPPRSRYRIDEKARFQPRDLLRHWEALLAILLVLVCAVNGLLLPHFFDPYNLADS 63 Query: 60 TFNFTEKAMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGL 119 TFNF+EKAMIA MALL+I EID+SV+AIIALAS AMG A Q G+ GL+L+ I TG Sbjct: 64 TFNFSEKAMIALPMALLIICREIDISVSAIIALASVAMGLANQAGVPPLGLLLVAIATGT 123 Query: 120 ACGVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVF 179 ACG+ NG LV+ L LPSIVVTIG+MSLFRG++ +VLGDQA+ +YP +GQGY V Sbjct: 124 ACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQYPEVLGDWGQGYFFDVL 183 Query: 180 SFEFVLFIVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSG 239 FV++++ AV+FA+LLH T +GR++YAIGNN AARFSG+ V+R + LF+LTG M+G Sbjct: 184 PRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAARFSGVAVDRYRLALFVLTGAMAG 243 Query: 240 IAAVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFG 299 +AA LT R+GSTRP+IA GWELE++T+V+LGG+SI GG GV +++ VMG++T+G Sbjct: 244 LAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIAGGTGSIGGV-MLSVLVMGMLTYG 302 Query: 300 LGLLNLPGIVMSIFIGLLIIVTIAIPIIAR 329 L L N+PGI+M+I +G L++ TIAIP + R Sbjct: 303 LALANIPGIIMTIVVGALLLATIAIPRLLR 332 Score = 25.4 bits (54), Expect = 0.002 Identities = 17/74 (22%), Positives = 34/74 (45%) Query: 76 LVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLP 135 + + E+++ I+ S A G G+ LV+ + GLA G++++++ Sbjct: 260 IAMGWELEIITVVILGGVSIAGGTGSIGGVMLSVLVMGMLTYGLALANIPGIIMTIVVGA 319 Query: 136 SIVVTIGTMSLFRG 149 ++ TI L RG Sbjct: 320 LLLATIAIPRLLRG 333 Lambda K H 0.330 0.145 0.423 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: 371 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 337 Length of database: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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 (21.8 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