Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PP_0221 PP_0221 methionine ABC transporter periplasmic-binding lipoprotein (metQ-like protein)
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Putida:PP_0221 Length = 266 Score = 141 bits (356), Expect = 1e-38 Identities = 95/262 (36%), Positives = 131/262 (50%), Gaps = 4/262 (1%) Query: 1 MKKLLAAFSAVAA-LGLTA-AQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFT 58 ++KL +A+A LGL A A AAE L + T A L K+G+++K+ EF+ Sbjct: 2 LEKLFRPVAAIAIILGLCAGALAAEPLKIGTTSA-FAIPLEAAVEEAHKQGLEVKLIEFS 60 Query: 59 DYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDEL 118 D++ PNV ++ +D N+FQH P+L+ A G +LV I +G YS KYK EL Sbjct: 61 DWIAPNVSLNSGDIDVNYFQHIPFLENAKAAAGFNLVPYAPGIINNVGLYSKKYKSFAEL 120 Query: 119 PSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATL 178 P GA+V I ND N GR LLLL KAG+I LK AT DI+ NPK +KI ++EA L Sbjct: 121 PEGASVAIANDPINSGRGLLLLAKAGLITLKPGVGYKATEADILANPKKLKILQVEAVQL 180 Query: 179 PRVLTQVDMALINTNYALEAKLNPTKDALAIEG-SDSPYVNILVARPDNKDSDAMQKLAK 237 R D+ Y A AL +G + YV V RP +KD + K Sbjct: 181 VRAYDDADLVQGYPAYIRLANTFDATSALLFDGLENKEYVIQFVIRPQSKDDPRLAKFVD 240 Query: 238 ALHSAEIKQFIQEKYKGAVVPA 259 + + + K G + A Sbjct: 241 IYQHSPVVRAALNKAHGKLYQA 262 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: 165 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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