Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 126 bits (317), Expect = 8e-34 Identities = 98/313 (31%), Positives = 163/313 (52%), Gaps = 19/313 (6%) Query: 66 LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125 +L L++++ A L + S +F ++ +IL++S + +LSIGM+ VI TGGIDL Sbjct: 36 MLGLALVIGAVLSLLSPYFLTE-------SNIFNILDQSVVIGILSIGMTFVILTGGIDL 88 Query: 126 SVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLL 185 SVG+V ++G V L + D + I G++ G G ++G L+ + + V TL + Sbjct: 89 SVGSVAGLSGIVLG--LALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGM 146 Query: 186 MVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLL----LRKT 241 M GR +A + + I+ ++I G+P V L F+ LL L T Sbjct: 147 MAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVL----FLGFAYLLAWGYLTYT 202 Query: 242 ALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLW 301 G I A+G N +A+R G+ + Y ++G AA+A S A I D G Sbjct: 203 KGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDP-LTGNG 261 Query: 302 LELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGL-PAKFNLLIKAIVIL 360 +ELDA+ AVVIGGA+L GGR S++ +++G LI+ + + + G+ P I +I+I+ Sbjct: 262 MELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIM 321 Query: 361 TVLLLQSAKFRRQ 373 +L+ + + R + Sbjct: 322 ALLVERLVRARSE 334 Lambda K H 0.323 0.136 0.379 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: 323 Number of extensions: 33 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: 405 Length of database: 335 Length adjustment: 30 Effective length of query: 375 Effective length of database: 305 Effective search space: 114375 Effective search space used: 114375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Apr 09 2024. 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