Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PP_0112 PP_0112 methionine ABC transporter, periplasmic binding protein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Putida:PP_0112 Length = 256 Score = 421 bits (1083), Expect = e-123 Identities = 216/260 (83%), Positives = 234/260 (90%), Gaps = 4/260 (1%) Query: 1 MKKLLAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDY 60 MKKLLA +AVAA + A++LTVAATPVPHAEILN VKP LAKEGV+LK+KEFTDY Sbjct: 1 MKKLLAVAAAVAAF----SAQADTLTVAATPVPHAEILNFVKPQLAKEGVELKVKEFTDY 56 Query: 61 VQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPS 120 +QPNVQV+EKRLDANFFQHQPYLDEFNKAKGT LV+V GVHIEPLG YS+K KKLDEL S Sbjct: 57 IQPNVQVAEKRLDANFFQHQPYLDEFNKAKGTSLVSVAGVHIEPLGVYSTKIKKLDELSS 116 Query: 121 GATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPR 180 GATVVIPNDATNGGRALLLLDKAGVIKLKDNK+I +T KD+ +NPKN+K RELEAAT+PR Sbjct: 117 GATVVIPNDATNGGRALLLLDKAGVIKLKDNKNILSTVKDVAENPKNVKFRELEAATIPR 176 Query: 181 VLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALH 240 VLTQVD ALINTNYALEAKLNP KDALAIEGSDSPYVNILVARPDNKDSD M+KLA ALH Sbjct: 177 VLTQVDAALINTNYALEAKLNPEKDALAIEGSDSPYVNILVARPDNKDSDDMKKLAAALH 236 Query: 241 SAEIKQFIQEKYKGAVVPAF 260 S E+KQFI EKYKGAVVPAF Sbjct: 237 SPEVKQFIIEKYKGAVVPAF 256 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: 307 Number of extensions: 11 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: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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