Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Pf6N2E2_3926 Methionine ABC transporter substrate-binding protein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3926 Length = 275 Score = 138 bits (347), Expect = 1e-37 Identities = 89/244 (36%), Positives = 124/244 (50%), Gaps = 4/244 (1%) Query: 13 ALGL--TAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVSEK 70 ALGL +A AA++ T A L +K+G+ +++ EF+D++ PNV ++ Sbjct: 22 ALGLFSSALFAADAPLKIGTTAAFAIPLEAAVEEASKQGLKVELVEFSDWIAPNVSLASG 81 Query: 71 RLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVVIPNDA 130 +D N+FQH P+L+ A G DLV I +G YS KYK DELP GA+V I ND Sbjct: 82 DIDVNYFQHIPFLENAKAAAGFDLVPFAPGIINNVGLYSKKYKSFDELPEGASVAIANDP 141 Query: 131 TNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRVLTQVDMALI 190 N GR L LL KAG+I LK AT DIV NPK +KI ++EA L R D+ Sbjct: 142 INSGRGLQLLAKAGLISLKPGVGYKATEDDIVANPKKLKILQVEAVQLVRAYEDADLVQG 201 Query: 191 NTNYALEAKLNPTKDALAIEGSD-SPYVNILVARPDNKDSDAMQKLAKAL-HSAEIKQFI 248 Y AK AL +G D YV V +P +K+ + K HS ++ + Sbjct: 202 YPAYIRLAKTFDASSALLFDGLDHKEYVIQFVIQPKSKNDPRLIKFVDIYQHSPAVRAAL 261 Query: 249 QEKY 252 + + Sbjct: 262 DKAH 265 Lambda K H 0.314 0.131 0.354 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: 169 Number of extensions: 7 Number of successful extensions: 1 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: 260 Length of database: 275 Length adjustment: 25 Effective length of query: 235 Effective length of database: 250 Effective search space: 58750 Effective search space used: 58750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 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