Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 234 bits (597), Expect = 3e-66 Identities = 142/368 (38%), Positives = 214/368 (58%), Gaps = 25/368 (6%) Query: 9 VWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVA 68 + K F +A+R++ L V+ GE + LGPSGCGKTT LR+IAGLE + G I + ++ Sbjct: 25 IHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDIS 84 Query: 69 DPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLG 128 ++P +RD +VFQSYAL+P++T+ +N+A+ L K+ + EI RV E+ + G Sbjct: 85 ------WLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAG 138 Query: 129 LTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQ 188 L + P +LSGGQ+QRVAL RA+ P + L+DEPLS LDA +RVR+RAE+++LQ+Q Sbjct: 139 LPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQ 198 Query: 189 LGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFL 248 +G+TTI VTHDQ EA++M DRI VMN GV++QVG+P E+Y++PA+ FVA F+G Sbjct: 199 VGITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK------ 252 Query: 249 DAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFAQVRVPGEN 308 V + FR+ + + E +G +V +RPED A + P Sbjct: 253 -VNVLRGQALGGKRFRVGKMEIECEASEGSFRLGEDVSLYLRPEDRV-AEHLEAGTPYR- 309 Query: 309 LVRAVVEIVENLGSERIVHLRVG-------GVTFVGSFRSESRVREGVEVDVVFDMKKIH 361 + +V VE LG I + G+ F + + + EG +D+ +I Sbjct: 310 -LGVLVNKVEFLGGLCIAEVSAEALGGQSLGLHFSLNQMHDLGICEGRRIDIALRASRIR 368 Query: 362 IFDKTTGK 369 +F +TG+ Sbjct: 369 VF--STGR 374 Lambda K H 0.323 0.142 0.406 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: 353 Number of extensions: 15 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: 372 Length of database: 377 Length adjustment: 30 Effective length of query: 342 Effective length of database: 347 Effective search space: 118674 Effective search space used: 118674 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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