Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Keio:14980 Length = 377 Score = 166 bits (419), Expect = 9e-46 Identities = 91/222 (40%), Positives = 134/222 (60%), Gaps = 6/222 (2%) Query: 48 VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107 V+D+SL+I GEIF ++G SG GKSTL+R P++G I++DG D+ Q+ LR Sbjct: 35 VDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVP-PYLRP- 92 Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPH 167 I+M+FQS+ L PH +V N+A+GLK K A R + V ++ + + PH Sbjct: 93 ----INMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPH 148 Query: 168 QLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITH 227 QLSGG RQRV LAR+LA ++L+DE ALD +R MQ +++++ + + T V +TH Sbjct: 149 QLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTH 208 Query: 228 DLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 D +EA+ + RIAI+ GK +Q+G P EI P Y F+ Sbjct: 209 DQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFI 250 Lambda K H 0.321 0.138 0.387 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: 220 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 276 Length of database: 377 Length adjustment: 28 Effective length of query: 248 Effective length of database: 349 Effective search space: 86552 Effective search space used: 86552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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