Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 130 bits (326), Expect = 6e-35 Identities = 72/214 (33%), Positives = 109/214 (50%), Gaps = 1/214 (0%) Query: 172 EGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALI 231 EG+ FFN++ + +PA +I + A YAL F G LL AL++ +P Q+ L+ Sbjct: 79 EGIGVYFFNSIAIVVPAVLISTAIGALNGYALTKWRFKGSELLFALMLFGCFIPFQVVLL 138 Query: 232 PLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIF 291 P+ +G+ G L H FG+ RN+ V +P +++ AK+DGA F+IF Sbjct: 139 PMAQTLGWLGLSSSRAGLILVHVIFGIAFTTLFFRNFYVAVPTELVSAAKLDGAGFFRIF 198 Query: 292 TKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWE 351 +I+LP+S P + I+QF WND L F T TV N +V T + Sbjct: 199 WRILLPVSAPIIVVSVIWQFTQIWNDFLFGVAFSAHNTQPVTVALNNLVN-TSTGAREYN 257 Query: 352 ILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 + AA ++ L+V+ ++ VRGL AGSVK Sbjct: 258 VDMAAAMIAALPTLIVYVLAGKYFVRGLTAGSVK 291 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: 249 Number of extensions: 14 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: 292 Length adjustment: 28 Effective length of query: 357 Effective length of database: 264 Effective search space: 94248 Effective search space used: 94248 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 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