Align ABC transporter related (characterized, see rationale)
to candidate WP_000942251.1 HK29_RS01475 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000382825.1:WP_000942251.1 Length = 254 Score = 231 bits (589), Expect = 1e-65 Identities = 116/247 (46%), Positives = 174/247 (70%), Gaps = 8/247 (3%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 L V++I K+FG+ VL+ ++L +QGDV+ ILG SGSGK+TFLRCLN LE D G ++LA Sbjct: 2 LQVEHIAKTFGERQVLEDVNLQVNQGDVVVILGPSGSGKTTFLRCLNHLEKADSGRLTLA 61 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 G+ + + ++ + +R + VFQ++NL+++ T LEN++EG + +K + Sbjct: 62 GKTYDLAKLS--------KKDILEIRQKTAFVFQHYNLFANKTALENILEGLIVARKVPK 113 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 E+++ AE+ L KVGL + +YP+ LSGGQQQR+ IARA+A+ P+V+L DEPTSALDPE Sbjct: 114 EEALKRAESALEKVGLLAYKDYYPSQLSGGQQQRIGIARAIAVKPEVILLDEPTSALDPE 173 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 LVG+VL V++ LA EG TM+VVTHEMGFAR V+N V+F+ G++ + P + F + + Sbjct: 174 LVGDVLDVLKQLAGEGVTMVVVTHEMGFARDVANHVIFMDGGRIVEENNPHDFFSRPQEE 233 Query: 249 RFRQFVS 255 R +QF++ Sbjct: 234 RTKQFLA 240 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: 161 Number of extensions: 3 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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 24 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