Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 244 bits (623), Expect = 2e-69 Identities = 136/299 (45%), Positives = 191/299 (63%), Gaps = 14/299 (4%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYF-------- 52 M + +Q L N L GS YAL+ALGYT+VYG++ LINFAHGDI+M+GA+I +F Sbjct: 1 MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60 Query: 53 LINSFQMNFFVALIVA----MLATAILGVVIEFLAYRPLRH--STRIAVLITAIGVSFLL 106 L+ F + + AL + ML TA +GV +E +AYRPLR + R+ V+ITA+ +L Sbjct: 61 LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL 120 Query: 107 EYGMVYLVGANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGK 166 E G + L+GA+ R P + V Y G +S+TN+++ ++ + ++ LLQ IV +T++G Sbjct: 121 ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM 180 Query: 167 AMRAVSVDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKS 226 AMRAV+ D A LMGI ++ I FTF LGS AG AG+L A+ Y L+P MG G K+ Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240 Query: 227 FVAAVLGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285 F+AAV+GGIG I GA +GGF++ +E AF S FRD + ILL+IL RP G+ G Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLFG 299 Lambda K H 0.330 0.146 0.407 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: 16 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: 292 Length of database: 306 Length adjustment: 27 Effective length of query: 265 Effective length of database: 279 Effective search space: 73935 Effective search space used: 73935 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: 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