Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Pf1N1B4_1701 Methionine ABC transporter substrate-binding protein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1701 Length = 269 Score = 135 bits (341), Expect = 7e-37 Identities = 91/257 (35%), Positives = 129/257 (50%), Gaps = 6/257 (2%) Query: 2 KKLLA--AFSAVAALGLTAAQ--AAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEF 57 KKLL+ + ALGL ++ AA++ T A L K+G+ +++ EF Sbjct: 3 KKLLSHPVKALALALGLFSSVTFAADAPLKVGTTAAFAIPLEAAVEEANKQGLKVELVEF 62 Query: 58 TDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDE 117 +D++ PNV ++ +D N+FQH P+L+ A G DLV I +G YS KYK DE Sbjct: 63 SDWIAPNVSLASGDIDVNYFQHIPFLENAKAAAGFDLVPFAPGIINNVGLYSKKYKSFDE 122 Query: 118 LPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAAT 177 LP GA+V I ND N GR L LL KAG+I LK AT +DI+ NPK IKI ++EA Sbjct: 123 LPEGASVAIANDPINSGRGLQLLAKAGLITLKPGVGYKATEEDIIANPKKIKILQVEAVQ 182 Query: 178 LPRVLTQVDMALINTNYALEAKLNPTKDALAIEGSD-SPYVNILVARPDNKDSDAMQKLA 236 L R D+ Y +K AL +G D YV V +P +K + K Sbjct: 183 LVRAYDDADLVQGYPAYIRLSKTFDASSALLFDGLDHKEYVIQFVIQPKSKTDPRLIKFV 242 Query: 237 KAL-HSAEIKQFIQEKY 252 HS ++ + + + Sbjct: 243 DIYQHSPAVRAALDKAH 259 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: 162 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: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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