Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 209 bits (531), Expect = 1e-58 Identities = 126/306 (41%), Positives = 174/306 (56%), Gaps = 17/306 (5%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ + + I K YG L G+ + + GE LLG SGCGK+ LL +IAG P G I Sbjct: 1 MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60 Query: 61 LIGERSVLG------VHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAV 114 IG V V P RD+ +VFQ YA++P++SVA NIG+ L++ +P AE + V Sbjct: 61 SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120 Query: 115 RDTARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRT 174 +T ++ + L +R PSQLSGGQ+QRVA+ RALV P + L DEPL NLDA LR EMR Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180 Query: 175 ELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVM-RDGRIEQLAAPDEVYDRPATLYVAGF 233 E+K L + L T++YVTHDQ A+ ++ R+A+M G I Q+ P E+++RPA +V F Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240 Query: 234 VGSPPMNILDAEMTANGLKIEGCEEVLP--LPAAFNGAAWAGRRVKVGIRPEALRLAAGS 291 +G N L A + G E+ +P LP + W G RP +RLA Sbjct: 241 MG--VANFLPARRRGMAMLAAGGEQPVPWGLPDG-DAEHW-----MAGFRPSDVRLARQG 292 Query: 292 EAQRLT 297 + R T Sbjct: 293 DGLRGT 298 Lambda K H 0.320 0.136 0.385 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: 324 Number of extensions: 14 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: 360 Length of database: 366 Length adjustment: 29 Effective length of query: 331 Effective length of database: 337 Effective search space: 111547 Effective search space used: 111547 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 (21.8 bits) S2: 49 (23.5 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