Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF3013 HP15_2957 sugar ABC transporter, permease protein
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__Marino:GFF3013 Length = 308 Score = 139 bits (351), Expect = 8e-38 Identities = 103/364 (28%), Positives = 166/364 (45%), Gaps = 83/364 (22%) Query: 4 RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63 R L LV+ P+ + +GV +YG++ LW + + + P FVG + Y +L Sbjct: 24 RWLPKLVVAPTFVLIGVGIYGYM---LWTGVLSFTSS-----SFLPVYDFVGFDQYAKLM 75 Query: 64 TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123 + R+ + +NL F F+ L +G++LA+ +D+ R EG RT++L+PMALS + Sbjct: 76 A---NDRWLTASINLGIFGGLFVLSCLVIGVILAIFLDQRIRQEGAIRTIYLYPMALSMI 132 Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGLVLL 183 VTGT+W+W+L P G+ L +G SF WL + + + YT ++ Sbjct: 133 VTGTVWKWILNPSLGLEKLMHDWGWTSFSFDWLVSSDMAI---------YTIVMA----- 178 Query: 184 YVAYTAYREGERRRALWGLASAGVLLLWAFAFGQGLRLLPYPEVHGFSLALVGVILAAVW 243 A+W + + L A G ++ V G SL L+ Sbjct: 179 --------------AVWQASGFVMALFLAGLRGVDSSIIRAARVDGASLPLI-------- 216 Query: 244 QMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIAL 303 + ++I P L P+ SA++VL HIA+ Sbjct: 217 -----------------------------------YWKIILPSLRPVFFSAVMVLAHIAI 241 Query: 304 KIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQ 362 K FDLV AM AG TD+PA++MY F Q G+A +L+L + ++VPYL ++ Sbjct: 242 KSFDLVMAMTAGGPGYSTDLPAVFMYAHTFTRGQMGLGSASAMLMLGAILALIVPYLYSE 301 Query: 363 LRKE 366 LR++ Sbjct: 302 LREK 305 Lambda K H 0.331 0.146 0.458 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: 346 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 369 Length of database: 308 Length adjustment: 28 Effective length of query: 341 Effective length of database: 280 Effective search space: 95480 Effective search space used: 95480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 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