Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_108401790.1 B9Z44_RS04225 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_003063475.1:WP_108401790.1 Length = 309 Score = 273 bits (698), Expect = 4e-78 Identities = 142/302 (47%), Positives = 199/302 (65%), Gaps = 9/302 (2%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M+ +QQ++NGL LGS+Y LVA+GYTMVYGII +INFAHG++ M+G + V +L + Sbjct: 1 MDVLLQQVINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMIGALCSWSVIGLLQPL 60 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 P VLLL+ +V+A + + N+ IE++AYRPLR + +LAPLITAIGMSI L Sbjct: 61 MPDTPGWVLLLISMVLASIAAAALNYAIEKIAYRPLRNAPKLAPLITAIGMSILLQTLAM 120 Query: 121 VTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 + P KP P ++ + ++ G ++ Q++I+ +TAV L + ++VNRT LGRA RAT Sbjct: 121 IVWKPNYKPFPTLLPTTPFEIGEAVITPTQLMILGLTAVALAVLSWLVNRTKLGRAMRAT 180 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 ++ ++A+L+GV D IS TF++GA LA +AG M+ M YG A GF PG+KAFTAAV Sbjct: 181 AENPRVASLMGVKPDVVISATFIIGAVLATIAGVMWAMNYGTAHHAMGFLPGLKAFTAAV 240 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVLIFKPTGI 291 GGIG+L GAV GGLL+GLIES+ S Y Y D+ F +L L +P+G+ Sbjct: 241 FGGIGNLGGAVVGGLLLGLIESIGSGYLGELTGGVLGSHYTDILAFVVLIITLTLRPSGL 300 Query: 292 LG 293 LG Sbjct: 301 LG 302 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: 351 Number of extensions: 18 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: 309 Length adjustment: 27 Effective length of query: 273 Effective length of database: 282 Effective search space: 76986 Effective search space used: 76986 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