Align MalF, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 3609627 Dshi_3010 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q97UG4 (322 letters) >FitnessBrowser__Dino:3609627 Length = 339 Score = 155 bits (392), Expect = 1e-42 Identities = 104/326 (31%), Positives = 172/326 (52%), Gaps = 17/326 (5%) Query: 3 TFFVVITVNFILPRLMPGSALAVVISLIEGQNGVAATAGSSAIALEVSQLEAAFGLTPAP 62 T F+ T+ +++PR P +++S + G A A S AI ++QL A FGL P Sbjct: 19 TVFIAATLIWLIPRFSPVDPAEIMLSRMAAGGG--AVADSEAI---LAQLRADFGLND-P 72 Query: 63 WYVQYAHYIQGIFTLNLGASITYYPTPVLSIILSGLPWTLFLVVVGAIIAFFLGSYLGSI 122 VQY Y+ + T NLG S +PTPV +I LPWTL L+++ +I F +G+ LG+ Sbjct: 73 LIVQYLKYMGNLLTFNLGISTASFPTPVSVLIAQALPWTLGLMILSVVITFVIGNALGAF 132 Query: 123 AGFNRRSRKDLVILIITSILAALP---SFVILMYLEM----WLSVQHGIFLISFPSKINT 175 + R + V++ I ++P S ++LMY+ WL + L P Sbjct: 133 MVWERTPKIWKVVIPTFMIFTSIPPILSGLLLMYIFSITLRWLPLTGSYGLTVEPGWDWA 192 Query: 176 SPNSIMALSRFYTLPIIALMFTSLSGFVLGMRNNMLHTIRDNYVTYAEILGLDHNRIR-K 234 +S++ TLP ++++ + + LGMR M+ ++YV A+ GL + K Sbjct: 193 FISSVIEHG---TLPALSIIVVTFGFWTLGMRGLMISVQGEDYVNLAKAKGLKPRYVLYK 249 Query: 235 MVYKNSLLPNITAFAIILGLAISQSLTVEGLLTTPGVGFFFGLALTSKDLPLLQGIFLFI 294 + +N++LP ITAFA+ +GL +S + VE + G+G A+ +D ++QG+ I Sbjct: 250 YMVRNAILPQITAFALKIGLLVSGQILVERIFGYNGMGKLLYDAILDQDFAVIQGVSYII 309 Query: 295 AIMLILSIAIVEAIYTILDPRARVSE 320 +M LS+ +V+ IY ++DPR R+SE Sbjct: 310 ILMTALSVFLVDLIYPLIDPRIRLSE 335 Lambda K H 0.328 0.142 0.410 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: 339 Number of extensions: 18 Number of successful extensions: 3 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: 322 Length of database: 339 Length adjustment: 28 Effective length of query: 294 Effective length of database: 311 Effective search space: 91434 Effective search space used: 91434 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: 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