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 GFF1916 PGA1_c19480 ABC transporter, inner-membrane protein
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Phaeo:GFF1916 Length = 297 Score = 244 bits (624), Expect = 1e-69 Identities = 123/281 (43%), Positives = 183/281 (65%), Gaps = 15/281 (5%) Query: 1 MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW---- 56 M R +Y FL + A FFL+P+Y+V++T+LK I L V QWP +++ AW Sbjct: 19 MRRIAIYVFLSVAAAFFLMPIYIVIVTSLKTMPEIRLGNVLQWPQTWSVDAWIKAWDTAC 78 Query: 57 -----EAFRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPY 111 E + F NS+ + + + ++S G+L GY+L W FRG+ + FA++LFG F+PY Sbjct: 79 TGLQCEGIKVGFWNSMRILLPSLVVSITAGALCGYILTFWTFRGAEIFFAILLFGAFVPY 138 Query: 112 QSILIPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAG 171 Q+++ P+ + + GLYG+L G+VLVH I+G+PI+TLIFRNYYS +P E+ +AAR+DGAG Sbjct: 139 QALIFPMIRIFSATGLYGTLPGIVLVHTIFGLPIMTLIFRNYYSTLPSEIFKAARVDGAG 198 Query: 172 FFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLA----GG 227 FF +F +V+LP+S P VV AI Q T IWN++L + E+ P+TV L + GG Sbjct: 199 FFSVFWYVLLPISTPIIVVAAILQVTGIWNDYLLGLIFGGRENMPMTVQLNNIVNSVRGG 258 Query: 228 EAVKWNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 + ++N+ MA +L AL L VY + GR+F+RG+ AG+VKG Sbjct: 259 K--EYNVNMAATLLTALVPLTVYFVSGRWFVRGIAAGAVKG 297 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: 301 Number of extensions: 12 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: 297 Length adjustment: 26 Effective length of query: 242 Effective length of database: 271 Effective search space: 65582 Effective search space used: 65582 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