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 Pf1N1B4_595 Glucose ABC transport system, inner membrane component 1
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_595 Length = 314 Score = 115 bits (288), Expect = 2e-30 Identities = 77/242 (31%), Positives = 129/242 (53%), Gaps = 29/242 (11%) Query: 152 SFPWLATREQVLVFDWNR-------LPFYTALVVGLVLLYVAYTAYREGERRRA------ 198 S+ W+ ++ + + D +R L + + +G+ L+ + A +R R Sbjct: 68 SYKWVGLQQYIRLMDNDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRT 127 Query: 199 --LWGLASA----GVLLLWAFAFGQGL-RLLPYPEVHGFSL--------ALVGVILAAVW 243 L+ +A + G W G GL ++L GF L + +++AAVW Sbjct: 128 VYLYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVW 187 Query: 244 QMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIAL 303 Q SG+ MA++LAGLRG+ ++ AA+VDGAS ++ +++ P L P+ SA ++L HIA+ Sbjct: 188 QASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAI 247 Query: 304 KIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQ 362 K FDLV AM AG +D+PA++MY F Q G+A +++L + ++VPYL ++ Sbjct: 248 KSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAILVPYLYSE 307 Query: 363 LR 364 LR Sbjct: 308 LR 309 Score = 92.4 bits (228), Expect = 1e-23 Identities = 60/160 (37%), 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: 30 RWLPKLVLAPSMLIVLVGFYGYIIWTFVLSFTN--------SSFMPSYKWVGLQQYIRLM 81 Query: 64 TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123 + R+ + NL F F+ SL LG+ LA+ +D+ R EGF RTV+L+PMALS + Sbjct: 82 D---NDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMI 138 Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVL 163 VTGT W+WLL P G++ + +G WL +++V+ Sbjct: 139 VTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVV 178 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: 379 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: 314 Length adjustment: 28 Effective length of query: 341 Effective length of database: 286 Effective search space: 97526 Effective search space used: 97526 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