Align RhaQ (characterized, see rationale)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 132 bits (331), Expect = 2e-35 Identities = 93/308 (30%), Positives = 158/308 (51%), Gaps = 26/308 (8%) Query: 31 LLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAII 90 LL + V++ + + +P FL A ++ + + M+A A L++++ IDLSVA+ + Sbjct: 1 LLALLTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNL 60 Query: 91 ALASTAMGA------AVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTM 144 AL+ A+ +G+ +L+ + GL G+ NG L+ L+LP IVVT+G+M Sbjct: 61 ALSGMMSALLAMHFPALPVGV----FILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSM 116 Query: 145 SLFRGISYIVLGDQ--AYGKYPADFAYF------GQGYVVWVFSFEFVLFIVLAVLFAIL 196 S++RG+ +++ G + PADF F G ++VW+ + V+A+ F L Sbjct: 117 SVYRGMVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHLVWLGA-----LAVVAIWF--L 169 Query: 197 LHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSI 256 T FGR +YAIGN+ AA + GI + L+G M+G+A +R I Sbjct: 170 ARHTRFGRDLYAIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEI 229 Query: 257 AQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGL 316 A G+EL V+ V+GG+SI GG G V+ A + ++ L ++ + S GL Sbjct: 230 AYGFELTVIAACVIGGVSIAGGVGQVSGA-VLGALFLSVINNALPIMRISPFWQSALTGL 288 Query: 317 LIIVTIAI 324 +I+ + + Sbjct: 289 VILCAVVL 296 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: 297 Number of extensions: 19 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: 337 Length of database: 323 Length adjustment: 28 Effective length of query: 309 Effective length of database: 295 Effective search space: 91155 Effective search space used: 91155 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