Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 174 bits (442), Expect = 2e-48 Identities = 100/249 (40%), Positives = 145/249 (58%), Gaps = 13/249 (5%) Query: 21 RSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNR 80 + K L++ R +K D V A V+D+SL+I GEIF ++G SGSGKSTL+R Sbjct: 16 QEKVLLKIERVSKLFDDVRA-------VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAG 68 Query: 81 LIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGE 140 PTSG I +DGEDI L I+M+FQS+ L PH +V N+A+GLK Sbjct: 69 FERPTSGRIYLDGEDITDLPP------YERPINMMFQSYALFPHMTVAQNIAFGLKQDKL 122 Query: 141 SKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALD 200 K +R + V ++ Y + PHQLSGG RQRV LAR+LA ++L+DE ALD Sbjct: 123 PKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALD 182 Query: 201 PLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSP 260 +R +MQ +++E+ + + T V +THD +EA+ + RI+I+ DG + Q G+P +I SP Sbjct: 183 KKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESP 242 Query: 261 ADEYVDRFV 269 + F+ Sbjct: 243 NSRMIAEFI 251 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: 234 Number of extensions: 7 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: 378 Length adjustment: 28 Effective length of query: 248 Effective length of database: 350 Effective search space: 86800 Effective search space used: 86800 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