Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 326 bits (835), Expect = 7e-94 Identities = 182/354 (51%), Positives = 234/354 (66%), Gaps = 5/354 (1%) Query: 2 SALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDIL 61 S + R++ R+G VE LK +++ ++ GEFLVLLG+SGCGKSTLLN IAGL E + G I Sbjct: 11 SHVSARDLSVRFGAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIW 70 Query: 62 IGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLL 121 I + +V PKDR +AMVFQSYALYP ++V N+ FGL M +VP+AE DK V + AR+L Sbjct: 71 INDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAARVL 130 Query: 122 QIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQ 181 Q+E LLDR+P +LSGGQRQRVAIGRALVR VFLFDEPLSNLDAKLR E+R ELKRLHQ Sbjct: 131 QLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVELKRLHQ 190 Query: 182 MLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNI 241 L T++YVTHDQ+EA+TLA RIAVM+DG ++QL +P+E+Y RPA YVA FVG P MN Sbjct: 191 ELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNF 250 Query: 242 LDAEMTANG-LKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 ++ +T +G ++ E E L + A G V++GIRPE + A A V Sbjct: 251 VNGVVTESGAIQTEDFELALDQCNLASTPA-PGTEVEIGIRPEHVHPA---NAGGFMLDV 306 Query: 301 EVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESG 354 +VEL G E + VG+ I P T + G A +F ++G Sbjct: 307 GMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTG 360 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: 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: 360 Length of database: 363 Length adjustment: 29 Effective length of query: 331 Effective length of database: 334 Effective search space: 110554 Effective search space used: 110554 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