Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_029134157.1 A3GO_RS0115370 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000428045.1:WP_029134157.1 Length = 293 Score = 166 bits (419), Expect = 8e-46 Identities = 104/300 (34%), Positives = 166/300 (55%), Gaps = 10/300 (3%) Query: 2 EYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIF 61 + +Q LL G+T+GS Y LV +G+ ++Y ++NF+ G+ M+G +A+ L++ Sbjct: 3 DQILQFLLTGITVGSTYALVGLGFAIIYNASDVVNFSQGEFVMIGAMSAV----ALSAGD 58 Query: 62 AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121 GLP L + A+L+T+L ++R A P RG+ + +I IG SI L + Sbjct: 59 TGLP----LWAAALAAVLITTLVGMALQRFAIXPARGASVVTTIIITIGASIFLRGVALL 114 Query: 122 TQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 G +PP + GN +V + + ++ AVL+ Y T LG+A A Sbjct: 115 VWGKDLFALPPFSGNEPIXIGNATVLPQSLWVMGGAAVLVFGAQYFFTHTTLGKAILACS 174 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240 ++ A L+G+NV + + + + AAL A+AG + + AS++ G G+K F+AA+L Sbjct: 175 CNKTAAHLVGINVGVMLLVAYGLSAALGAMAGIL-VAPITFASYDTGVMLGLKGFSAAIL 233 Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300 GG+G+ GAV GGLL+GLIESL + + YKD F IL VL F+P+G+ G+ VE+V Sbjct: 234 GGMGNPMGAVAGGLLLGLIESLSAGLISSGYKDAIGFIILLLVLFFRPSGLFGKASVERV 293 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: 304 Number of extensions: 25 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: 300 Length of database: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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 24 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