Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate RR42_RS14410 RR42_RS14410 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS14410 Length = 259 Score = 326 bits (835), Expect = 3e-94 Identities = 155/253 (61%), Positives = 195/253 (77%) Query: 2 SREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGT 61 S E+LKV L MRFGGLLAV+G+ V+ +V A+IGPNGAGKTTVFNC+ GFY+PT G Sbjct: 6 SAELLKVSGLQMRFGGLLAVDGIDFDVRRDEVFAIIGPNGAGKTTVFNCVGGFYKPTAGE 65 Query: 62 ILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTP 121 ++LDG I LP H +AR+G+VRTFQN+RLFK +T VENLL+AQH + + GLF TP Sbjct: 66 VMLDGHSIARLPSHQVARRGLVRTFQNIRLFKQLTVVENLLVAQHLQVRSGLLRGLFATP 125 Query: 122 AFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 A+R++EREA+E A WL+++ L ANR AGTL+YG QRRLEIARCM+T PR+LMLDEPA Sbjct: 126 AYRRAEREALERAALWLERMGLRGVANREAGTLSYGHQRRLEIARCMITNPRLLMLDEPA 185 Query: 182 AGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQI 241 AGLNP+E +L LI LR EH ++VLLIEHDM LVM +SD I+V+ G P+ G P ++ Sbjct: 186 AGLNPQEKVELSQLIDQLRREHKISVLLIEHDMSLVMGVSDRILVMEHGRPILVGKPAEV 245 Query: 242 RDNPEVIKAYLGE 254 R++P VIKAYLGE Sbjct: 246 RNDPRVIKAYLGE 258 Lambda K H 0.321 0.138 0.398 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: 249 Number of extensions: 6 Number of successful extensions: 1 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: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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