Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_106713880.1 CU102_RS25515 ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >NCBI__GCF_003010955.1:WP_106713880.1 Length = 331 Score = 205 bits (522), Expect = 1e-57 Identities = 118/312 (37%), Positives = 196/312 (62%), Gaps = 16/312 (5%) Query: 66 LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125 +LAL +L+L NL +F + +L L + + ++++GM+LVIATGGIDL Sbjct: 26 ILALVLLILFNLAFTRNFATMQ--------TLNVNLTQVCTIVIVAVGMTLVIATGGIDL 77 Query: 126 SVGAVMAIAGAVCANLLL---VPDISLVTVIAAGLIVGL----LAGCINGGLVSFLGIQP 178 SVG++MAI+GA+ + L VP S+ + A +++ + L G NG L++ IQP Sbjct: 78 SVGSLMAISGALAPMIFLGKIVPIDSVGIAVVAAMVISVGVAGLFGLFNGWLIAKFRIQP 137 Query: 179 IVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLL 238 IVATL+L +AGRG+AQ++ G + TF+ P F IG+G+ G+P+ V +++ ++ + +L Sbjct: 138 IVATLVLFIAGRGIAQVMTNGNLQTFRVPQFQFIGLGRVFGVPVQVVLMLLLVIAAAWVL 197 Query: 239 RKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNA 298 ++T G I A+G N +A+ GI ++KL Y I+GLCA +AG++ A SDAN Sbjct: 198 KRTVFGRQIIAIGGNERAAELSGIAVSTVKLVVYTISGLCAGVAGLVVIAINSSSDANLV 257 Query: 299 GLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKA-I 357 GL +ELDA+ AV +GG L+GG+ +++ +++GA+ IQ + T++ +G+P L++KA I Sbjct: 258 GLGMELDAIAAVAVGGTLLSGGKATIVGTLLGAMTIQLVRYTLLANGVPDAAALVVKAGI 317 Query: 358 VILTVLLLQSAK 369 ++L V + Q + Sbjct: 318 IVLAVWIQQQGR 329 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: 348 Number of extensions: 24 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: 331 Length adjustment: 30 Effective length of query: 375 Effective length of database: 301 Effective search space: 112875 Effective search space used: 112875 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 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