Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110206119.1 DNK54_RS06380 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_003194585.1:WP_110206119.1 Length = 299 Score = 140 bits (354), Expect = 3e-38 Identities = 99/314 (31%), Positives = 157/314 (50%), Gaps = 29/314 (9%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M F + + GL LG+IY L+A+G+ MVY G++NFA G+ LG F L + Sbjct: 1 MTQFAELTIAGLALGAIYSLIAVGFVMVYRSSGLLNFAQGEFATLGAF--------LMTT 52 Query: 61 FAGL-----PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITL 115 FA PVA+LL V++++A+ M IERV R L G I I + L Sbjct: 53 FAAWAVLPWPVALLLTVLVMMAVGMG------IERVIMRKLLGRPPFIGSIVTIFVGFLL 106 Query: 116 SNFIQVTQGP--RNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALG 173 S + G R P P + + G + +L ++ I++ VL+ +++ RT +G Sbjct: 107 SVAVLWIYGSSTRAMPTPWDPVKIVEVGGVEFTLTNLVTILVAIVLIGTLAFVMQRTPMG 166 Query: 174 RAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVK 233 A RA D++ A LG+ V++ + +T+ + A+L AVAG M+ A+ G + Sbjct: 167 MAMRAVADDQEAAFALGIPVERLLGLTWGIAASLGAVAGVFLAMFPRSATVAMGLL-AFR 225 Query: 234 AFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAY-------FTIAYKDVATFAILAFVLIF 286 AF A ++GG+ S GA+ GG +GL++ Y F I + V F ++ L+ Sbjct: 226 AFPAVIIGGLESPVGAIIGGSALGLLQVHGEYYVNPHLGDFGIGFHLVLAFIVMIAFLMI 285 Query: 287 KPTGILGRPEVEKV 300 KP G+ G E+E+V Sbjct: 286 KPHGLFGTKELERV 299 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: 287 Number of extensions: 18 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: 299 Length adjustment: 27 Effective length of query: 273 Effective length of database: 272 Effective search space: 74256 Effective search space used: 74256 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