Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 207 bits (527), Expect = 4e-58 Identities = 122/294 (41%), Positives = 176/294 (59%), Gaps = 7/294 (2%) Query: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 L +DL + GE + LGPSGCGK+T+LR+IAGLE + G++ G ++ LPA ER+ Sbjct: 35 LRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASERDYG 94 Query: 80 MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139 +VFQ+YAL+P++++ +N+A+GL K AEI RV E+ A+ L + P +SGGQ Sbjct: 95 IVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKYPSQLSGGQ 154 Query: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199 QQR A+ARA+ P + L DEPLS LDA +R +LR +I+RL +++ TT+ VTHDQ EA+ Sbjct: 155 QQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTHDQEEAL 214 Query: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETA 259 +++DR+++M G I Q G+P E+Y P + F A F+G +N L G Q G+ F Sbjct: 215 SMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLRG--QALGGKRFRVGK 270 Query: 260 HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILG 313 + E RL V L +RP+ R+A E V V VE LG Sbjct: 271 MEIECEASEGSFRL--GEDVSLYLRPED-RVAEHLEAGTPYRLGVLVNKVEFLG 321 Lambda K H 0.321 0.137 0.403 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: 342 Number of extensions: 9 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: 406 Length of database: 377 Length adjustment: 31 Effective length of query: 375 Effective length of database: 346 Effective search space: 129750 Effective search space used: 129750 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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