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_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 151 bits (382), Expect = 1e-41 Identities = 95/269 (35%), Positives = 151/269 (56%), Gaps = 15/269 (5%) Query: 8 GFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRP-----K 62 G LL++A L P+ +V ++ T + P P +F E F Sbjct: 17 GGLLVLALVSLAPLLWMVSVSVMPAGEAT---TFPPPLTPSHVTFANYHELFARTGMGVN 73 Query: 63 FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122 F NS++++V+ TL S L+ ++ GY AK F G LF +++ + IP Q ++PLF M Sbjct: 74 FANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLM 133 Query: 123 KSIGLYGSLFGLVL--VHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVI 180 K +GL S G+++ + ++GI +V R Y IPDEL+EAAR+DGAG IF ++ Sbjct: 134 KQLGLVNSFGGVIVPALATVFGIFLV----RQYARSIPDELLEAARMDGAGEMRIFFQIV 189 Query: 181 LPLSVPAFVVVAIWQFTQIWNEFLF-AVTLTRPESQPITVALAQLAGGEAVKWNLPMAGA 239 LP+ P V ++I+ F WN+F++ + LT E + VALA L+ + + MAGA Sbjct: 190 LPMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVEMMMAGA 249 Query: 240 ILAALPTLLVYILLGRYFLRGLLAGSVKG 268 ++ +P L +++LL RY+++GL+ GSVKG Sbjct: 250 VVTVIPVLALFLLLQRYYIQGLMLGSVKG 278 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: 10 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: 268 Length of database: 278 Length adjustment: 25 Effective length of query: 243 Effective length of database: 253 Effective search space: 61479 Effective search space used: 61479 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