Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AZOBR_RS19485 AZOBR_RS19485 methionine ABC transporter substrate-binding protein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__azobra:AZOBR_RS19485 Length = 259 Score = 192 bits (487), Expect = 8e-54 Identities = 103/260 (39%), Positives = 149/260 (57%), Gaps = 1/260 (0%) Query: 1 MKKLLAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDY 60 +K L + A L ++ A +L + + P+ EIL + AKEG+ ++ EFTD+ Sbjct: 1 VKAFLTSIVTAALLTVSTGAGAAALKLGVSAGPYGEILEYTAKIAAKEGLKAEVIEFTDW 60 Query: 61 VQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPS 120 PN + +DAN FQHQP+LD K +G D+V V + P+G Y+ K + L +L Sbjct: 61 NMPNAALQSGDIDANNFQHQPFLDNQIKQRGYDIVPVAKSIVVPMGIYAKKVQSLADLKE 120 Query: 121 GATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPR 180 GA+V IPND TNG RAL LL KAGVI LKD + + DI NPK IK+ EL+AA LPR Sbjct: 121 GASVSIPNDPTNGARALFLLAKAGVIGLKDGAGLNTSIADIASNPKKIKLVELDAAQLPR 180 Query: 181 VLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALH 240 L VD ++I NYA+ A L P K AL +E S + + R D + A+++ + Sbjct: 181 SLDDVDASVITLNYAVLAGLTP-KTALVLEDDQSKWHLVWAVRKDRAEDPAIKRFIELYR 239 Query: 241 SAEIKQFIQEKYKGAVVPAF 260 SAE++ FI ++ G ++P + Sbjct: 240 SAEVRDFINTRFNGTIIPTW 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: 167 Number of extensions: 5 Number of successful extensions: 2 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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