Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 244 bits (623), Expect = 3e-69 Identities = 135/306 (44%), Positives = 198/306 (64%), Gaps = 15/306 (4%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 + + +V+K + +K A+ + L V+ EFV +LGPSGCGKTT LR+IAG + ++G+I I Sbjct: 10 IEVSHVSKFFGDKT-ALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRI 68 Query: 66 DGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILG 125 GK + P R + VFQ YAL+PH+ VY+N+AFGLKL+K PK I ++V+ A K++G Sbjct: 69 SGKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVG 128 Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185 + + R LSGGQ+QRVA+ RAIV P+V L DEPL+ LD K+R M+ ELK++H Sbjct: 129 MTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKS 188 Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFV 245 L T +YVTHDQ EA+T++D IVVM +G+IQQIGTP +IYN P N FVA FIG N + Sbjct: 189 LGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNIL 246 Query: 246 NARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPEN 305 N ++ + ++ G + + ++ +++ IRPED+Y +F ++ + Sbjct: 247 NGTMIHDK---LVRFCGTEFEC---VDEGFGENTPVDVV--IRPEDLY--IFPVSEMAQ- 295 Query: 306 TITGVV 311 +TGVV Sbjct: 296 -LTGVV 300 Lambda K H 0.319 0.138 0.387 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: 426 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: 369 Length of database: 463 Length adjustment: 31 Effective length of query: 338 Effective length of database: 432 Effective search space: 146016 Effective search space used: 146016 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