Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Koxy:BWI76_RS23390 Length = 375 Score = 320 bits (819), Expect = 5e-92 Identities = 193/392 (49%), Positives = 250/392 (63%), Gaps = 35/392 (8%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 M E+ N + K Y N +V DL I + EF+V VGPSGC KSTTLRM+AGLE I+ G Sbjct: 1 MAEVIFNKLEKVYSNGFK-AVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGG 59 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 E++I ++VN+ APK R IAMVFQNYALYPHM+V +N+AFGLKL K+ I+ +V EAA Sbjct: 60 EVRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAA 119 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 +IL L E L+R P LSGGQ QRVA+GRAIV+ VFL DEPLSNLDAKLR SMR I+ Sbjct: 120 KILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISD 179 Query: 181 IHRRI-----GATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYN 235 +H+++ ATT+YVTHDQTEAMT+ DRI +M +G + QV TP LY+ Sbjct: 180 LHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMK----------LGHIMQVDTPDNLYH 229 Query: 236 RPANKFVAGFIGSPAMNFFDVTIKDGHLVSKDG-LTIAVTEGQLKM---LESK--GFKNK 289 +P N FVAGFIG+P MN I+ LV + G L + V +G L + L+SK KN+ Sbjct: 230 KPKNMFVAGFIGAPEMN-----IRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQ 284 Query: 290 NLIFGIRPEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARV---DA 346 + FG+RPE +S S E + + + E+V E +G E +YLK+ E ARV +A Sbjct: 285 QVFFGVRPEFVSIS---DEPFAEGSCTGEMVRVENMGHEFFVYLKVADYELTARVPSDEA 341 Query: 347 RDFHEPG--EKVSLTFNVAKGHFFDAETEAAI 376 + E G KV F++ K H FDA+TE I Sbjct: 342 KPMIEKGLHRKVHFKFDLNKCHIFDAKTEQNI 373 Lambda K H 0.318 0.135 0.375 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: 414 Number of extensions: 23 Number of successful extensions: 6 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: 377 Length of database: 375 Length adjustment: 30 Effective length of query: 347 Effective length of database: 345 Effective search space: 119715 Effective search space used: 119715 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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