Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011801051.1 PNAP_RS08255 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000015505.1:WP_011801051.1 Length = 291 Score = 165 bits (417), Expect = 1e-45 Identities = 101/301 (33%), Positives = 163/301 (54%), Gaps = 11/301 (3%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M F+Q L +GL G+IY L A+G+T+++ G INFA G+ ML F + L S+ Sbjct: 1 MTDFLQLLFSGLATGAIYALAALGFTLLWQASGTINFAQGEFVMLPAF----MMLGFMSL 56 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 A + V+ +L V+L + +L W +R PL + ++ IG+SI + N ++ Sbjct: 57 GAPMLVSFVLTVLLAILVL-----GWVFKRGVVDPLFKYGMMPIVVATIGLSIFMRNGVR 111 Query: 121 VTQGPRNKPIPPMVSS-VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 P P + + ++ ++V+L+ I V+ ++ + +T GRA +A Sbjct: 112 AGYSAEAHPFPSLFADKLFNIAGVTVTLQDIGTFVLAMAIVMGTQAFLAKTVTGRAMQAV 171 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 Q+ + A++LG+NV + I TF + A LA A + Y +A F+ G G KAF AA+ Sbjct: 172 AQNTESASVLGINVPRMIFYTFAINAVLAVAAALLVTPTY-LAKFDMGEGLGNKAFFAAI 230 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEK 299 +GG + GA+ GGLL+G+ E+L +AY + AYKD I V++FKP G+LG+ E K Sbjct: 231 IGGFNNSRGALVGGLLVGVCENLAAAYISPAYKDAVALVIFMVVILFKPQGLLGKKEERK 290 Query: 300 V 300 V Sbjct: 291 V 291 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: 257 Number of extensions: 9 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: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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