Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 162 bits (409), Expect = 1e-44 Identities = 90/217 (41%), Positives = 132/217 (60%), Gaps = 10/217 (4%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 + ++ V++ FE T AL +D +R+ +F+T+LGPSGCGK+T+LR+V+G + TSG Sbjct: 8 IELRGVTKTFED-----TVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSG 62 Query: 64 RVLLDGAPVEGPGAER---GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFI 120 V ++G V E+ VFQ+Y LFP +T+ N+ FGL+ +G+ + R + Sbjct: 63 EVRINGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDAL 122 Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180 V L F P+QLSGG QQR AIARA+ N+P +LL+DEPF ALD + R MQ + Sbjct: 123 RMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKH 182 Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIK 217 + T +FVTHD +EA M++RV V + GRI+ Sbjct: 183 LQRQLGITFVFVTHDQEEAFAMSDRVVVMN--EGRIE 217 Lambda K H 0.322 0.136 0.394 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: 259 Number of extensions: 9 Number of successful extensions: 3 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: 259 Length of database: 399 Length adjustment: 28 Effective length of query: 231 Effective length of database: 371 Effective search space: 85701 Effective search space used: 85701 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