Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 8501186 DvMF_1920 ABC transporter related (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Miya:8501186 Length = 249 Score = 278 bits (711), Expect = 8e-80 Identities = 146/250 (58%), Positives = 178/250 (71%), Gaps = 3/250 (1%) Query: 1 MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60 M + +P+I L K FG +VLRG+ + P +V+ IIGPSG GKST LRC+NRLE I Sbjct: 1 MKTCESPMIEIRNLHKRFGQNEVLRGIDLTVCPGEVVVIIGPSGSGKSTALRCINRLEEI 60 Query: 61 SGGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPM 120 + G++ V G DL D + +R GMVFQ FNLFPH++VL N+ L P +V R P Sbjct: 61 TSGKVVVDGHDLYDPATD---INYVRTEAGMVFQQFNLFPHMSVLHNVTLGPIRVRRTPR 117 Query: 121 AEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPE 180 AEA L L+KVGL KA YPDQLSGGQKQRVAIAR L M+P++LLFDEPTSALDPE Sbjct: 118 AEADRLGLALLEKVGLADKATAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPE 177 Query: 181 LVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSD 240 LVGEVL VM+ LA EGMTM +VTHEM FAREV++RV F +QG I+EEG P+E F PK+ Sbjct: 178 LVGEVLEVMRALALEGMTMVIVTHEMGFAREVADRVIFIDQGRIQEEGPPDEFFSAPKNP 237 Query: 241 RLRAFLSRIQ 250 RLR FL R++ Sbjct: 238 RLREFLGRVR 247 Lambda K H 0.321 0.139 0.397 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: 221 Number of extensions: 6 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: 252 Length of database: 249 Length adjustment: 24 Effective length of query: 228 Effective length of database: 225 Effective search space: 51300 Effective search space used: 51300 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: 46 (22.3 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