Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_013402068.1 CALHY_RS00465 carbohydrate ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_000166355.1:WP_013402068.1 Length = 280 Score = 137 bits (345), Expect = 3e-37 Identities = 81/266 (30%), Positives = 136/266 (51%), Gaps = 7/266 (2%) Query: 10 LLLMAGFF----LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFR--PKF 63 LL++ G F L P+ ++ +L + + + + P+PP + ++ AW + F Sbjct: 15 LLVVLGLFSIGQLFPLVWLIDFSLCKSGDVYGANILKIPNPPQFINYYLAWRDGKIPQYF 74 Query: 64 QNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMK 123 NSV++ V++ LL L + GY + ++ S + +L G+ IP + L+P F + Sbjct: 75 INSVIVNVTSVLLVVLFSLMMGYAFVRMEWKWSNKVLTYVLLGLMIPIHATLLPNFVIFR 134 Query: 124 SIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPL 183 + + S F L++ +V + +P + + IP L E+A IDG G F I +ILPL Sbjct: 135 QLKMLDSYFALIIPYVAFSLPQAVFLMTGFIGSIPRALEESAIIDGCGIFRILFQIILPL 194 Query: 184 SVPAFVVVAIWQFTQIWNEFLFAVT-LTRPESQPITVALAQLAGGEAVKWNLPMAGAILA 242 S PA V V + F WNEF+ A T LT + + + ++ AG A + + A + Sbjct: 195 SKPAIVTVTVTTFLNTWNEFIMAATYLTSDKFRTLPFSVYNFAGQYASNYAVQFAVMTIV 254 Query: 243 ALPTLLVYILLGRYFLRGLLAGSVKG 268 ALP+L+VYI L +G+ G+VKG Sbjct: 255 ALPSLIVYIALNEQVTKGVTLGAVKG 280 Lambda K H 0.330 0.146 0.461 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: 243 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 268 Length of database: 280 Length adjustment: 25 Effective length of query: 243 Effective length of database: 255 Effective search space: 61965 Effective search space used: 61965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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