Align ABC transporter related (characterized, see rationale)
to candidate SMc02260 SMc02260 ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Smeli:SMc02260 Length = 284 Score = 318 bits (814), Expect = 1e-91 Identities = 157/252 (62%), Positives = 198/252 (78%) Query: 5 APVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 A A++V ++HK FG VLKG+SL A QGDVI+I+G SGSGKST LRC+N+LE P G Sbjct: 31 AAQAIAVTDLHKRFGPLEVLKGVSLSARQGDVIAIIGGSGSGKSTLLRCINMLELPSAGQ 90 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ 124 +S+ GEE++MK G G L P+DR+QV R+R+QLGMVFQ+FNLW HMT+L+N+IE P+ V Sbjct: 91 ISVHGEEIRMKPDGHGGLMPADRKQVQRIRTQLGMVFQSFNLWQHMTILQNVIEAPVHVL 150 Query: 125 KRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSA 184 +++AE+VE AEALL +VGL EKR YPA LSGGQQQR AIARALA+ P VMLFDEPTSA Sbjct: 151 GKTKAEAVETAEALLRRVGLYEKRDAYPAFLSGGQQQRAAIARALAIQPLVMLFDEPTSA 210 Query: 185 LDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVE 244 LDPELVGEVL V+ LA E RTM++VTHEM FAR V+N ++FLH G +E G P+ +F Sbjct: 211 LDPELVGEVLSVIGDLAREERTMVLVTHEMKFARDVANHIVFLHNGVIEEQGPPEAIFGA 270 Query: 245 CKSDRFRQFVSS 256 KS+R ++F+SS Sbjct: 271 PKSERLKKFISS 282 Lambda K H 0.318 0.133 0.377 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: 220 Number of extensions: 6 Number of successful extensions: 1 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: 263 Length of database: 284 Length adjustment: 25 Effective length of query: 238 Effective length of database: 259 Effective search space: 61642 Effective search space used: 61642 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 (21.7 bits) S2: 47 (22.7 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