Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_004266034.1 C665_RS01200 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000310185.1:WP_004266034.1 Length = 288 Score = 126 bits (316), Expect = 7e-34 Identities = 89/293 (30%), Positives = 149/293 (50%), Gaps = 19/293 (6%) Query: 4 FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63 F+ Q+LN L G + LVA G T+V+GI+G+IN AHG +M+G + A LTS+ Sbjct: 6 FLIQILNALQYGLLLFLVASGLTLVFGIMGIINLAHGSFYMIGAYLAF----ALTSLTGN 61 Query: 64 LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123 L +A++L + L + +E++ + L L ++ G+ + +T Sbjct: 62 LMLAIVLGIPLAFG------FGALLEKLLFVHLYKRDHLQQVLLTYGLILIFEELRSLTV 115 Query: 124 GP--RNKPIPPMVS-SVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 G IP + S S+ N+S + +++I V+ L W+++ RT LG RA Sbjct: 116 GDDVHGVAIPDLFSASIALSDNLSYPVYRLVISVVCIALAVGLWWLMQRTRLGMMIRAGS 175 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVK--AFTAA 238 +R+M LGVN+D F +G ALAA+AG ++ ++S G V +F Sbjct: 176 FNREMVQSLGVNIDLLYRTVFALGVALAALAG---MLAAPISSVYPGMGGNVLIISFVVV 232 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGI 291 V+GGIGS+ GA+ LL+G ++ + +A + ++A VL+++P GI Sbjct: 233 VIGGIGSVWGALVAALLVGFADT-FGTILLPELAGLAVYLLMAVVLLWRPEGI 284 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: 284 Number of extensions: 20 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: 288 Length adjustment: 26 Effective length of query: 274 Effective length of database: 262 Effective search space: 71788 Effective search space used: 71788 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