Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF3965 HP15_3905 lipoprotein, YaeC family
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Marino:GFF3965 Length = 260 Score = 374 bits (961), Expect = e-109 Identities = 187/260 (71%), Positives = 217/260 (83%), Gaps = 2/260 (0%) Query: 1 MKKLLAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDY 60 +KK LAA +A A + A AAE L+VAATPVPHAEIL VKP LA++GV+L +K FTDY Sbjct: 3 LKKTLAALAAAATF--SGAVAAEELSVAATPVPHAEILEFVKPQLAEQGVELDVKVFTDY 60 Query: 61 VQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPS 120 +QPN+QV +KR+DANFFQHQPYLDEFN+ +GT+LV VTGVH+EP GAYSSK + LDEL Sbjct: 61 IQPNIQVDQKRMDANFFQHQPYLDEFNEGRGTNLVTVTGVHVEPFGAYSSKIESLDELKE 120 Query: 121 GATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPR 180 GA V IPND TNGGRALLLL KAGVI LKD ITATP+DI DNPK++ +ELEAATLPR Sbjct: 121 GAVVAIPNDPTNGGRALLLLQKAGVITLKDESKITATPRDIADNPKDLDFKELEAATLPR 180 Query: 181 VLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALH 240 +L QVD+ALINTNYALEA LNP++DAL IEGS+SPYVNILVARPDNKDS+AMQKLA AL Sbjct: 181 ILNQVDLALINTNYALEAGLNPSEDALVIEGSESPYVNILVARPDNKDSEAMQKLAAALK 240 Query: 241 SAEIKQFIQEKYKGAVVPAF 260 S ++ FI EKY+GAVVPAF Sbjct: 241 SDAVRDFIMEKYEGAVVPAF 260 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: 269 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: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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