Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 224 bits (572), Expect = 2e-63 Identities = 130/288 (45%), Positives = 182/288 (63%), Gaps = 24/288 (8%) Query: 13 FGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEK 72 +G A+ + SL++ +GEF+ LLGPSG GK++ LR++AGL++P RG + + D Sbjct: 12 YGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDV------LRDGTD 65 Query: 73 GIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLR----KVPRQEIDQRVREVAELLG 128 + +P + RDI +VFQ YAL+PHMTV DNIAF L++R + R++I RV ++ + Sbjct: 66 LLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQ 125 Query: 129 LTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQ 188 L EL R P +LSGGQRQRVAL RA+ +P + L+DEP LDA++R +R L+ LQR Sbjct: 126 LEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRS 185 Query: 189 LGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFL 248 LG+TT+ VTHDQ EA+ + DR+ VMNRG ++QVG+P E+Y +PA FV GF+G N + Sbjct: 186 LGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGR--ANRI 243 Query: 249 DAIVTEDGFVDFGEFRLKLLPDQFEVLGEL--GYVGREVIFGIRPEDL 294 V D RL L F+ GEL GRE+ +RPE L Sbjct: 244 RGHVERD--------RLHLGGHSFQ--GELPGDLAGREIEAWLRPEHL 281 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: 365 Number of extensions: 14 Number of successful extensions: 3 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: 384 Length adjustment: 30 Effective length of query: 342 Effective length of database: 354 Effective search space: 121068 Effective search space used: 121068 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 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