Align ABC transporter (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 235 bits (599), Expect = 2e-66 Identities = 140/349 (40%), Positives = 207/349 (59%), Gaps = 24/349 (6%) Query: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 L++ ++K LRD+ L + GE + F+GPSGCGK+TLLR+IAGL++ G ++ Sbjct: 20 LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79 Query: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 GR ++ L ER G+VFQSYAL+P++++ +N+++GL K K ++ RV + + L Sbjct: 80 GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139 Query: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183 + P +LSGGQ+QRVA+ RA+A P +LL DEPLS LDA++RV++R EI RL ++ Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199 Query: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243 G T I VTHDQ EA++++D+IVV+N G +EQVG+P E+YERPAS FVA F+G ++N L Sbjct: 200 GITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLR 257 Query: 244 ARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPE-HVSLKAADGT---AGVV 299 + G+ V + + G +SL +RPE V+ GT GV+ Sbjct: 258 GQ-ALGGKRFRVGKME---IECEASEGSFRLGEDVSLYLRPEDRVAEHLEAGTPYRLGVL 313 Query: 300 VTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLH 348 V VE+LG +C EVSA G + L L+ +H Sbjct: 314 VNKVEFLGG--------------LCIAEVSAEALGGQSLGLHFSLNQMH 348 Lambda K H 0.320 0.137 0.394 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: 317 Number of extensions: 10 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: 381 Length of database: 377 Length adjustment: 30 Effective length of query: 351 Effective length of database: 347 Effective search space: 121797 Effective search space used: 121797 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