Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 225 bits (573), Expect = 2e-63 Identities = 135/354 (38%), Positives = 208/354 (58%), Gaps = 17/354 (4%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 ++D +L ++ E F+GPSGCGKTT LR+IAGLE T G++ R ++ +P +RD Sbjct: 35 LRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASERDYG 94 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 +VFQ+YAL+P++T+ +N+A+GL K+ KAEI RV E + + + P LSGGQ Sbjct: 95 IVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKYPSQLSGGQ 154 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 +QRVAL RA+ P + L+DEPLS LDA +RV++RAEIR+L +++ T I VTHDQ EA+ Sbjct: 155 QQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTHDQEEAL 214 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260 +M DRIVVM GVI+Q TP +Y +P + FVA F+G +N +RG+ + G F Sbjct: 215 SMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVLRGQAL-GGKRFRVGKM 271 Query: 261 SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM-TTYPDSVLQMQVE-----V 314 I EG + +G+ V L +RPED E + T Y VL +VE Sbjct: 272 EIECEASEGSF-------RLGEDVSLYLRPEDRVAEHLEAGTPYRLGVLVNKVEFLGGLC 324 Query: 315 VEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAETEES 368 + + +E S+G + + +++ + G + +A+ ++I +F +++ Sbjct: 325 IAEVSAEALGGQSLGLHFSLNQMHDLGICE-GRRIDIALRASRIRVFSTGRDQA 377 Lambda K H 0.321 0.138 0.395 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: 345 Number of extensions: 13 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: 384 Length of database: 377 Length adjustment: 30 Effective length of query: 354 Effective length of database: 347 Effective search space: 122838 Effective search space used: 122838 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