Align Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 159 bits (403), Expect = 6e-44 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 37/309 (11%) Query: 4 ASRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVF 63 AS G+ F +V+ + ++ P W ++SFK + + P L P ++E Y N+F Sbjct: 12 ASSPRGKRFAAAIVITYALIAILPILWICLTSFKTQEDAIAYPPVVLFQP-SMEGYVNLF 70 Query: 64 L----------------QANFGRNL-----------------LNSLIVAGGATLLSLVLG 90 Q + R++ +NSL++ G+T L++ LG Sbjct: 71 TIRSRQTPEFIASLPPAQTWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLG 130 Query: 91 VLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQTGLFNTHLGLILTYLLF 150 LAAYA R P + +++ +LS M P IAV ++L+ R GL ++++G+I+ Y Sbjct: 131 TLAAYAFSRFKVPLADDLLFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAV 190 Query: 151 TLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWN 210 + VW+L G+ +PRE EEAA VDG T LQ +KV+LP G+ T + I AWN Sbjct: 191 NVSLAVWLLKGFMDEIPREYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWN 250 Query: 211 EYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVVTVPLVVLVLVFQQRIV 270 EY FA T GD+ +T+PP I G + W ++ AA+ + VP+++ +V ++ ++ Sbjct: 251 EYAFASLLTSGDA-QTMPPFIPFIIGEGGQD--WPAVAAATTLFVVPILIFTVVLRKHLL 307 Query: 271 AGLTAGAVK 279 G+T GAV+ Sbjct: 308 RGITFGAVR 316 Lambda K H 0.329 0.145 0.439 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: 176 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 280 Length of database: 317 Length adjustment: 26 Effective length of query: 254 Effective length of database: 291 Effective search space: 73914 Effective search space used: 73914 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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