Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate WP_028743224.1 RL_RS19905 sugar ABC transporter permease
Query= TCDB::Q9KZ07 (334 letters) >NCBI__GCF_000009265.1:WP_028743224.1 Length = 319 Score = 166 bits (419), Expect = 9e-46 Identities = 110/335 (32%), Positives = 179/335 (53%), Gaps = 24/335 (7%) Query: 1 MTVAIDRATGKRRGDRTPRPGLGRRLKDGYQKHWYAYAMIAPVAVVIGVLVLYPLGYGLY 60 MT+ +A +RR + R G+ R++ + H YA + P V+ +++ YP+ Y + Sbjct: 1 MTILTGKAEARRRL-QPDRSGVLRKIWE----HRADYAYVLPAIAVMLIVIAYPIYYTIE 55 Query: 61 LTLTDANSLNSARTIGVNEIEATYKFVGLDNYADILWGPTAYDRFWSHFIWTIVWTAVCV 120 L+ N+ + + + FVGLDNY IL P FW+ T++WT Sbjct: 56 LSF-----FNTPPGLQLRD----KIFVGLDNYIAILTSPV----FWTVTSNTLIWTLGST 102 Query: 121 GLHFFIGLGLALLLNQKLRGRTFYRLILVLPWAVPTFVTVFGWRFML-ADQGIINSALDW 179 + F +G G AL L++ GR R IL++PW + + W+++ +D GII + L Sbjct: 103 LIAFVLGFGCALALHRDFLGRGILRAILIIPWVISAVAASYIWKWIYHSDFGIIGAVLVG 162 Query: 180 LHLPT--PAWLEDTFWQRFSAIMVNTWCGVPFMMVSLLGGLQSIDNSLYEASEMDGANAW 237 L L P +++ S I+VN W PF M+ ++ GLQ++ + L A+ +DGANAW Sbjct: 163 LGLADRPPNFIDSVSTVLPSLIVVNIWREFPFAMIMMMAGLQTVPDQLLRAARVDGANAW 222 Query: 238 QRFRYVTLPGLRSVSSTVVLLGIIWTFNQFAVIFLLFGNTAPDA-QILVTWAYQLGFGQQ 296 QRF +VT P LR+VS+ +LL + FN F + +++ G +A I +T Y+L FG+Q Sbjct: 223 QRFWHVTFPHLRNVSTVTILLLAVANFNSFIIPWIMTGGGPSNASHIWITHIYELAFGRQ 282 Query: 297 PRDFAQSAAYGILLLAILIVFTSFYRRWLNRNEQQ 331 + ++AY +LL IL+ FY R L+ NE++ Sbjct: 283 --RWGVASAYSVLLFLILMSLGYFYVRALSGNERK 315 Lambda K H 0.328 0.142 0.468 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: 30 Number of successful extensions: 5 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: 334 Length of database: 319 Length adjustment: 28 Effective length of query: 306 Effective length of database: 291 Effective search space: 89046 Effective search space used: 89046 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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