Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU0 (300 letters) >MicrobesOnline__882:206138 Length = 301 Score = 245 bits (626), Expect = 8e-70 Identities = 124/302 (41%), Positives = 195/302 (64%), Gaps = 3/302 (0%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 ME F+QQL NGL +G IY L+A+GYTMVYG++ +INFAHGD+F +G + VF L + Sbjct: 1 MEEFLQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAAL-GL 59 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 + AV +L++ + M + +L + +ERVAYRPLR S RL+ +++A+G SI N + Sbjct: 60 SGHVSGAVAVLLVTTMVMGLVALIGYLLERVAYRPLRSSSRLSAVVSALGASIFFQNAVM 119 Query: 121 VTQGPRNKPIPPMV--SSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178 + G + + P + + F + + L +I++ + L+ + + ++RT G A RA Sbjct: 120 LIYGAKFQVYPNDIRPTMAVSFFGMDIPLVRIMMFGASVALMLLLHFFIHRTRTGTAIRA 179 Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238 D+ A L+G++V++ I++ F++G AL AG M +YYG F G+ G+KAFTAA Sbjct: 180 VAIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTAA 239 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVE 298 +LGGIG++PGA+ GGLL+G+IE+L +AY +IA+KD F +L +LI +PTG+LG + Sbjct: 240 ILGGIGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGLLGERVAD 299 Query: 299 KV 300 K+ Sbjct: 300 KI 301 Lambda K H 0.329 0.143 0.421 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: 331 Number of extensions: 24 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: 300 Length of database: 301 Length adjustment: 27 Effective length of query: 273 Effective length of database: 274 Effective search space: 74802 Effective search space used: 74802 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