Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate 3609760 Dshi_3143 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::O51924 (295 letters) >FitnessBrowser__Dino:3609760 Length = 290 Score = 166 bits (421), Expect = 4e-46 Identities = 96/286 (33%), Positives = 163/286 (56%), Gaps = 12/286 (4%) Query: 12 REAKLGYLMILPLLTVVLVFIILPVMGTFWIS-----LHRDVTFIPEKPFVGLRNYL-RV 65 R+ L Y ++LP + VV I P++ +S L+R + + ++G NY Sbjct: 2 RDNTLKYFLVLPAVVVVFATAIWPLIEAARMSFTVGRLNRPGSL---EQYIGWENYAWAF 58 Query: 66 LSAREFWYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIIS 125 FW S +VT ++ V+V L T+L L AL+L + R + ++++P+A+ + Sbjct: 59 FEEPAFWNSVYVTALYTVVTVGLTTLLALGLALLLAPGGRLRVSAQTLLILPFAMSPALI 118 Query: 126 ARTWELMYNYSYGLFNWILSIL--GVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLA 183 ++ M+N +GLF+ ++ ++ V+WL P AF +V+ADVW PF+TL+L+ Sbjct: 119 GVSFRFMFNPEFGLFDAFFGVMIPPLADVSWLADPTLAFAVVVMADVWGWIPFLTLVLIG 178 Query: 184 GLQAIPQDLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGG 243 GL ++P+D EAA +DGAS + F+ +TLP L PVL V +IL++I +L+ FD +++LT G Sbjct: 179 GLASVPRDTIEAAQVDGASSWRVFRDVTLPQLGPVLAVVIILKSIFSLKTFDQVFMLTNG 238 Query: 244 GPGGATTSIS-LLAFNYYNLGDYGIGSAISILTFVLVLSFTIVYLK 288 GPG AT ++S + FN G G ++++ L + ++ T Y K Sbjct: 239 GPGTATQTLSHYIYFNGMKYGQIGYSASVAWLMVIPMIFLTYAYAK 284 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: 291 Number of extensions: 16 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: 295 Length of database: 290 Length adjustment: 26 Effective length of query: 269 Effective length of database: 264 Effective search space: 71016 Effective search space used: 71016 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