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 18060 b4032 maltose transporter subunit (NCBI)
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Keio:18060 Length = 296 Score = 89.7 bits (221), Expect = 6e-23 Identities = 81/281 (28%), Positives = 122/281 (43%), Gaps = 26/281 (9%) Query: 10 LLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW---------EAFR 60 LLL + P+ +VV +L++ T + P W+ ++ A Sbjct: 20 LLLFIAAIMFPLLMVVAISLRQGNFATGSLI---PEQISWDHWKLALGFSVEQADGRITP 76 Query: 61 PKFQ------NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSG-LLFALILFGMFIPYQS 113 P F NSV +A + + + + Y A+ F G LL +++F MF P Sbjct: 77 PPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMF-PAVL 135 Query: 114 ILIPLFQFMKSIGLYGSLFGL-----VLVHVIYGIPIVTLIFRNYYSEIPDELVEAARID 168 L+ L+ +G Y GL V+ + GI + + Y+ I L EAA +D Sbjct: 136 SLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALD 195 Query: 169 GAGFFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRP-ESQPITVALAQLAGG 227 GA + FR V+LPLSVP VV I F E A L R S + V + Q Sbjct: 196 GATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNP 255 Query: 228 EAVKWNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 + W A A+++ALP +V++L R+ + GL AG VKG Sbjct: 256 QNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296 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: 216 Number of extensions: 17 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: 268 Length of database: 296 Length adjustment: 26 Effective length of query: 242 Effective length of database: 270 Effective search space: 65340 Effective search space used: 65340 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 17 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