Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= SwissProt::P19566 (369 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 166 bits (419), Expect = 1e-45 Identities = 98/247 (39%), Positives = 141/247 (57%), Gaps = 10/247 (4%) Query: 20 KDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI-GE--TRMND---IPPA 73 +D + +I GE V +G SG GKST++RM+ L TSG + I GE MND + Sbjct: 47 QDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVR 106 Query: 74 ERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQLAHLLERKPKA 133 + MVFQS+AL PH++V +N +FGL++ G K+ QR Q E + L E P Sbjct: 107 RAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDE 166 Query: 134 LSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHD 193 LSGG +QRV + R L +P + L+DE S LD +R +M+ E+ +L + RT+++++HD Sbjct: 167 LSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHD 226 Query: 194 QVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFI-GSPKMNFLPVKVTATAIE 252 EAM + D+I +++ GRV QVG P E+ PAD +V F G N L AT Sbjct: 227 LDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIAT--- 283 Query: 253 QVQVELP 259 Q QV +P Sbjct: 284 QTQVTIP 290 Lambda K H 0.321 0.138 0.396 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: 325 Number of extensions: 14 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: 369 Length of database: 415 Length adjustment: 31 Effective length of query: 338 Effective length of database: 384 Effective search space: 129792 Effective search space used: 129792 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