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 WP_007695788.1 C447_RS16060 sugar ABC transporter permease
Query= TCDB::Q72KX3 (369 letters) >NCBI__GCF_000336675.1:WP_007695788.1 Length = 324 Score = 103 bits (256), Expect = 8e-27 Identities = 71/206 (34%), Positives = 107/206 (51%), Gaps = 16/206 (7%) Query: 176 LVVGLVLLYVAYTAYREGERRRALWGLASA------GVLLLWAFAFGQGLRLLPYPEVHG 229 LV+GL L V R E+ + ++ L A LW + + G+ + V Sbjct: 116 LVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWMYNYNSGVINIILDAVGI 175 Query: 230 FSLALVG--------VILAAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRR 281 + +G VI A +WQ SGYTM +YL+GL+ IP + EAA DGAS +++ R Sbjct: 176 GRIQFIGDPRFVLGAVIFALIWQFSGYTMIVYLSGLQSIPQDQFEAAATDGASTVKIYWR 235 Query: 282 VIFPMLAPITLSAMIVLGHIALKIFDLVFAMAGLDYAP--TDVPAIYMYLLAFRGNQFAK 339 VI P L ++SA +VL ALK F +++M G P +D+ A M AF+ +++ Sbjct: 236 VIIPQLKSASVSAAVVLMIFALKAFTFLYSMFGTYRPPNGSDILATLMVRQAFKFQEWSY 295 Query: 340 GAAIGILLLLLVAVVVVPYLATQLRK 365 AA+ LLLL+ VV+ PYL Q ++ Sbjct: 296 AAAVATLLLLMALVVIGPYLYYQYQR 321 Score = 66.6 bits (161), Expect = 9e-16 Identities = 49/142 (34%), Positives = 68/142 (47%), Gaps = 20/142 (14%) Query: 18 VGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYREL-FTGFVDVRFRQSVV 76 +G FVYG IG NL VSLTD+ G +Y +L F +V V+ Sbjct: 53 MGFFVYGGIGWNLLVSLTDYTG--------------FGSADYGDLDFEMYVQALSSPDVI 98 Query: 77 ----NLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFVVTGTIWRWL 132 N + F A L LGL LA+ +D+ R + +T++L PMALSFVVT W W+ Sbjct: 99 AASRNTFVLLVVFTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWM 158 Query: 133 LQPQGGV-NVLPTLFGLPPLSF 153 GV N++ G+ + F Sbjct: 159 YNYNSGVINIILDAVGIGRIQF 180 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: 299 Number of extensions: 15 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: 324 Length adjustment: 29 Effective length of query: 340 Effective length of database: 295 Effective search space: 100300 Effective search space used: 100300 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 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