Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_2749 PP_2749 putative Branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Putida:PP_2749 Length = 293 Score = 126 bits (316), Expect = 7e-34 Identities = 90/308 (29%), Positives = 158/308 (51%), Gaps = 23/308 (7%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M +F++ L+ GL G++Y LVAIG+ ++Y G+ NFA G A+++F LT + Sbjct: 1 MNFFLETLIGGLLAGTLYSLVAIGFVLIYKASGVFNFAQG---------AMLLFAALTFV 51 Query: 61 F---AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSN 117 GLP A L L + V+ M++ +L IER+ RPL ++ + +G+S + Sbjct: 52 SLHEQGLPFA-LALALTVLVMIVGAL---LIERLVLRPLVNRSQITLFMATLGLSFIIEG 107 Query: 118 FIQVTQGPRNKPIPPMVSSVYQF-GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQ 176 Q G + + + + V F G + +S ++ ++A+L+ + + N+T +G A Sbjct: 108 LAQGLMGAQVRALDLGIEDVPLFVGELMISQFDLVASGVSALLVAVLALLFNKTRIGVAL 167 Query: 177 RATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFT 236 RA D + A LG+N+++ I + + + VAG ++ GV F+ +KA Sbjct: 168 RAVADDTRAALSLGINLNRIWQIVWAVAGMVGLVAGLLWGARQGV-QFSLSLVV-LKALP 225 Query: 237 AAVLGGIGSLPGAVFGGLLIGLIESLWSAYF--TIAYKDVATFA-ILAFVLIF-KPTGIL 292 ++GG S+ GA+ GGL++G E+L AY I FA LA + ++ +P G+ Sbjct: 226 VLIIGGFTSIGGAIVGGLIVGAAENLAEAYIGPLIGGGITPWFAYFLALIFLYIRPAGLF 285 Query: 293 GRPEVEKV 300 G +E+V Sbjct: 286 GDRAIERV 293 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: 290 Number of extensions: 23 Number of successful extensions: 5 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: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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 17 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