Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012335138.1 M446_RS26265 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000019365.1:WP_012335138.1 Length = 306 Score = 436 bits (1120), Expect = e-127 Identities = 216/306 (70%), Positives = 258/306 (84%), Gaps = 6/306 (1%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 ME F QQL+NGLTLGSIYGL+AIGYTMV+GIIGMINFAHGD+FML F ALI FL+LT++ Sbjct: 1 MEVFAQQLINGLTLGSIYGLIAIGYTMVFGIIGMINFAHGDVFMLSAFIALIAFLLLTTV 60 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 V V L+++++VAM +T+LW W IER+AY+PLRGSFRLAPLI+AIG+SI LSNF+Q Sbjct: 61 LGIGSVVVALILVMIVAMALTALWGWAIERIAYQPLRGSFRLAPLISAIGVSIFLSNFVQ 120 Query: 121 VTQGPRNKPIPPMVSSVYQFGN------ISVSLKQIIIIVITAVLLTIFWYIVNRTALGR 174 V QG RNKP PPM+ V +++S KQI+I+ +TA+LL FWY+V T+LGR Sbjct: 121 VVQGARNKPTPPMLRDVIVLWTGENGYAVALSYKQILIMAVTAILLAGFWYLVQHTSLGR 180 Query: 175 AQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKA 234 AQRA EQDRKMA+LLG++VD+TIS+TFV+GAALAAVAGTMYL+YYGV SF+DGF PGVKA Sbjct: 181 AQRACEQDRKMASLLGIDVDRTISLTFVLGAALAAVAGTMYLLYYGVLSFSDGFVPGVKA 240 Query: 235 FTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 FTAAVLGGIGSLPGAV GGL+IGLIE+ WSAYF+I YKDVA F+ILA VLIF P+GILGR Sbjct: 241 FTAAVLGGIGSLPGAVLGGLIIGLIETFWSAYFSIEYKDVAAFSILAIVLIFMPSGILGR 300 Query: 295 PEVEKV 300 PEVEKV Sbjct: 301 PEVEKV 306 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: 421 Number of extensions: 12 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: 306 Length adjustment: 27 Effective length of query: 273 Effective length of database: 279 Effective search space: 76167 Effective search space used: 76167 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