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 HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 330 bits (846), Expect = 4e-95 Identities = 187/365 (51%), Positives = 239/365 (65%), Gaps = 13/365 (3%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA V ++ + K Y+ + + NL + D EF VL+GPSGCGK+T LRM+ GLEEI+ G+ Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 + I G+VVN + P +R IAMVFQ+YALYPHM VY+NMAFGLK+ K +ID R+R AA Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 IL I++LL R PR+LSGGQRQRVA+GRAIVR P++FLFDEPLSNLDA LRVQ R E+ KL Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 H +L ATI+YVTHDQVEAMT+ DKIVVM +G IQQ GTP E+Y P N+FVAGFIGSP M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 243 NFVNARVVR-GEGGLWIQ-ASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALA 300 NF V R + G+ ++ A G ++ D L + G+R E I + L Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLAD---VDPLGVTPGAAVTLGLRAEQIREGLGDGQ 297 Query: 301 PSPENTITGVVDVVEPLGSETILHVKV--GDDLIVASVNPRTQAKEEQKIDLVLDMTRMH 358 P + GVV++VE LG L+V + G D++V R Q I L + H Sbjct: 298 P-----LHGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNR-NVDIGQPIALSVHSHAFH 351 Query: 359 AFDKE 363 FD + Sbjct: 352 LFDAQ 356 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: 365 Number of extensions: 9 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: 377 Length adjustment: 30 Effective length of query: 339 Effective length of database: 347 Effective search space: 117633 Effective search space used: 117633 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 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