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 PfGW456L13_1895 Glucose ABC transport system, inner membrane component 1
Query= TCDB::Q72KX3 (369 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1895 Glucose ABC transport system, inner membrane component 1 Length = 302 Score = 116 bits (290), Expect = 9e-31 Identities = 58/129 (44%), 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+L V ++ Sbjct: 229 ILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTIL 288 Query: 356 VPYLATQLR 364 VPYL ++LR Sbjct: 289 VPYLYSELR 297 Score = 94.0 bits (232), Expect = 5e-24 Identities = 60/160 (37%), Positives = 89/160 (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 RWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTN--------SSFMPSYKWVGLQQYMRLM 69 Query: 64 TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123 + R+ + NL F F++ SL LG+ LA+ +D+ R EGF RTV+L+PMALS + Sbjct: 70 D---NDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMI 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: 340 Number of extensions: 12 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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