Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate H281DRAFT_01524 H281DRAFT_01524 D-methionine transport system substrate-binding protein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_01524 Length = 271 Score = 221 bits (564), Expect = 9e-63 Identities = 119/260 (45%), Positives = 164/260 (63%), Gaps = 6/260 (2%) Query: 7 AFSAVAALGLTAAQA---AESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQP 63 A + VAAL LT A L V P A+I +VV + A+EG+++K+ EF DYVQP Sbjct: 12 ALAGVAALSLTTTFAHADGPQLKVGTMSGPDAQIWSVVTKVAAREGLNVKVIEFNDYVQP 71 Query: 64 NVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGAT 123 N + LDAN FQHQP+LD K +G + V ++ P+G YS K+K L +LP GA Sbjct: 72 NAALDAGDLDANGFQHQPFLDSQIKQRGYKIANVGLTYVSPMGFYSKKFKSLKDLPEGAK 131 Query: 124 VVIPNDATNGGRALLLLDKAGVIKLK---DNKSITATPKDIVDNPKNIKIRELEAATLPR 180 V I ND +NG RALLLL K GVIKLK + ATP D+ +N K I++ EL+AA LPR Sbjct: 132 VGIQNDPSNGNRALLLLQKYGVIKLKPGVGTNGVNATPLDVAENHKKIRLVELDAAQLPR 191 Query: 181 VLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALH 240 L +D A INT+YA++A L PTKDA+AIE PY N++ R +++ ++KL A Sbjct: 192 ALDDLDAASINTDYAVKAGLQPTKDAIAIEDLKGPYANLIAVREKDRNQPWVKKLVAAYE 251 Query: 241 SAEIKQFIQEKYKGAVVPAF 260 S E++++I ++KGA++PAF Sbjct: 252 SDEVRKYIDTQFKGAIIPAF 271 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: 213 Number of extensions: 11 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: 271 Length adjustment: 25 Effective length of query: 235 Effective length of database: 246 Effective search space: 57810 Effective search space used: 57810 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