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 AO353_03390 AO353_03390 sugar ABC transporter permease
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03390 Length = 302 Score = 115 bits (287), Expect = 2e-30 Identities = 56/129 (43%), Positives = 88/129 (68%), Gaps = 1/129 (0%) Query: 237 VILAAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMI 296 +++AAVWQ SG+ MA++LAGLRG+ ++ AA+VDGAS ++ +++ P L P+ SA + Sbjct: 169 LVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFM 228 Query: 297 VLGHIALKIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVV 355 +L HIA+K FDLV AM AG +D+PA++MY F Q G+A +++L + ++ Sbjct: 229 ILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAIL 288 Query: 356 VPYLATQLR 364 VPYL ++LR Sbjct: 289 VPYLYSELR 297 Score = 92.0 bits (227), Expect = 2e-23 Identities = 59/160 (36%), Positives = 88/160 (55%), Gaps = 11/160 (6%) Query: 4 RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63 R L LVL PS+L V V YG+I +S T+ + P ++VGL+ Y L Sbjct: 18 RWLPKLVLAPSMLIVLVGFYGYIIWTFVLSFTN--------SSFMPSYKWVGLQQYVRLM 69 Query: 64 TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123 + R+ + NL F F+ SL LG+ LA+ +D+ R EGF RT++L+PMALS + Sbjct: 70 E---NDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRTIYLYPMALSMI 126 Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVL 163 VTGT W+WLL P G++ + +G WL +++V+ Sbjct: 127 VTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVV 166 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: 350 Number of extensions: 13 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: 302 Length adjustment: 28 Effective length of query: 341 Effective length of database: 274 Effective search space: 93434 Effective search space used: 93434 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 Apr 09 2024. 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