Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate H281DRAFT_05181 H281DRAFT_05181 putrescine transport system ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Burk376:H281DRAFT_05181 Length = 388 Score = 174 bits (442), Expect = 2e-48 Identities = 92/232 (39%), Positives = 139/232 (59%), Gaps = 6/232 (2%) Query: 38 VLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDIL 97 V+ + G V V ++LS+ GE+F ++G SG GKSTL+R L TSG IL+DGED+ Sbjct: 36 VVKKFGETVAVKQVNLSVKKGELFALLGSSGCGKSTLLRMLAGLETVTSGKILIDGEDLA 95 Query: 98 QLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVG 157 QL R ++M+FQS+ L PH +V NVA+GLK G K +R + V Sbjct: 96 QLPP------YRRPVNMMFQSYALFPHMTVESNVAFGLKQEGVPKAELKDRVQTALELVQ 149 Query: 158 LKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKT 217 + + N+ PHQLSGG +QRV LAR+L ++L+DE SALD IR Q +L+ + T Sbjct: 150 MGRFANRKPHQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKQIRQRTQIELVNILDT 209 Query: 218 LHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 + T + +THD +EA+ + R+A++ +G+++Q+GTP E+ P + F+ Sbjct: 210 VGVTCIMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVYEYPNSRFSAEFI 261 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: 223 Number of extensions: 10 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: 276 Length of database: 388 Length adjustment: 28 Effective length of query: 248 Effective length of database: 360 Effective search space: 89280 Effective search space used: 89280 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