Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_054655217.1 CES79_RS10005 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_002217945.1:WP_054655217.1 Length = 292 Score = 233 bits (593), Expect = 5e-66 Identities = 133/303 (43%), Positives = 182/303 (60%), Gaps = 14/303 (4%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAAL--IVFLVLT 58 M QQL+NGL+LGSIY L+A+GYTMVYGII +INFAHGDI+MLG F I + Sbjct: 1 MTTLFQQLINGLSLGSIYALLALGYTMVYGIIKLINFAHGDIYMLGAFWGYYTINYWHFN 60 Query: 59 SIFAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNF 118 IFA L+ AM++ + IE AYRPLR + R+ LITAIG+S L N Sbjct: 61 FIFA-----------LLSAMVVCAASGVIIEYFAYRPLRHAPRITALITAIGVSYFLENG 109 Query: 119 IQVTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177 + G + P ++ V Y + VS QI+I+ +L+ + I+ +T +GRA R Sbjct: 110 MSYLYGADTRDFPQVIKQVNYSLWGVRVSNIQILILATACLLMILLQLIIKKTKMGRAMR 169 Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237 A D A L+G+N++QTIS TF +G+++A AG + +YY G TPG+KAF A Sbjct: 170 AVSVDPDAAELVGININQTISFTFALGSSMAGAAGVLIGLYYNSIDPLMGMTPGIKAFVA 229 Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297 AV+GGIGS+PGA GG LIGL+E+ + AYKD A + +L +L+ P+GI G+ Sbjct: 230 AVVGGIGSVPGASLGGFLIGLLETAVQSVGLSAYKDAAVYLVLIIILLVLPSGIFGKNVK 289 Query: 298 EKV 300 EKV Sbjct: 290 EKV 292 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: 323 Number of extensions: 22 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: 292 Length adjustment: 26 Effective length of query: 274 Effective length of database: 266 Effective search space: 72884 Effective search space used: 72884 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