Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SMc04257 SMc04257 ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Smeli:SMc04257 Length = 305 Score = 136 bits (343), Expect = 7e-37 Identities = 78/217 (35%), Positives = 118/217 (54%), Gaps = 3/217 (1%) Query: 170 NSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLA 229 N +G++R F+N++ +T+P+ II I +A+ YALA F G L +++ +P Q+ Sbjct: 90 NCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQVM 149 Query: 230 LIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQ 289 + P++ + +G+ G + HT FGMP+ L RNY GLP ++ + A+VDGA + Sbjct: 150 IYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAGFWT 209 Query: 290 IFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIV-ELLGTRGG 348 I+ KI+LP+S P I Q WND L VF TV N IV + G + Sbjct: 210 IYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNIVNSVQGVKEY 269 Query: 349 NWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 N + AT ++ VPL V+F R VRG+ AG+VK Sbjct: 270 NVNMAAT--ILTGLVPLTVYFVSGRLFVRGIAAGAVK 304 Lambda K H 0.323 0.138 0.419 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: 277 Number of extensions: 10 Number of successful extensions: 2 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: 385 Length of database: 305 Length adjustment: 29 Effective length of query: 356 Effective length of database: 276 Effective search space: 98256 Effective search space used: 98256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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