Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_005457271.1 SACCYDRAFT_RS14745 ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >NCBI__GCF_000244975.1:WP_005457271.1 Length = 369 Score = 307 bits (786), Expect = 4e-88 Identities = 172/344 (50%), Positives = 231/344 (67%), Gaps = 10/344 (2%) Query: 63 LWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGG 122 +WP+LAL+ LL+ N+ + SFF+I QD LYGSLIDIL AP L+++GM+LVIAT G Sbjct: 18 VWPVLALAALLVVNVVVTPSFFDIRLQDGHLYGSLIDILKNGAPTLLIALGMTLVIATRG 77 Query: 123 IDLSVGAVMAIAGAV-CANLLLVPD----ISLVTVIAAGLIVGLLAGCINGGLVSFLGIQ 177 IDLSVGAV+AIAGAV C ++ D + + L + LL G NG LVS LGIQ Sbjct: 78 IDLSVGAVVAIAGAVACTSIAGANDPGGASAAFLAMTLALALCLLLGAWNGFLVSVLGIQ 137 Query: 178 PIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLL 237 PI+ATL+LM AGRG+A LI GQI+T + +AA+G G FL LP+ + I +G+ +L Sbjct: 138 PIIATLVLMTAGRGIAMLITDGQIVTVNNGTYAAVGAG-FLVLPVAILISLGVFVLVAVL 196 Query: 238 LRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANN 297 RKTALG+ IEAVG N ASR G+ ++I Y A LCA +AG++ +A++ +DANN Sbjct: 197 TRKTALGMLIEAVGVNPTASRLAGVRSRTIVWTVYVFAALCAGVAGLMISANVSAADANN 256 Query: 298 AGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAI 357 AGLW+ELDA+LAVVIGG AL+GGR+SL ++VGAL+IQTL TT+ G+P++ L+ KA+ Sbjct: 257 AGLWIELDAILAVVIGGTALSGGRYSLTGTLVGALLIQTLTTTVYTIGIPSEVTLVFKAL 316 Query: 358 VILTVLLLQSAKFRRQLSALFKSKRHADAKPAEKATSAKASAAT 401 V++ V LLQS K R AL + R A+ + + AT Sbjct: 317 VVIAVCLLQSPKAR----ALLRRNRTPAVAQADIGDAPEPRGAT 356 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: 365 Number of extensions: 21 Number of successful extensions: 3 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: 369 Length adjustment: 30 Effective length of query: 375 Effective length of database: 339 Effective search space: 127125 Effective search space used: 127125 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: 50 (23.9 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