Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 16237 b2129 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Keio:16237 Length = 308 Score = 181 bits (458), Expect = 3e-50 Identities = 100/249 (40%), Positives = 147/249 (59%), Gaps = 9/249 (3%) Query: 39 GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98 G V D +L +EG V++G SGSGKST ++++NRL+E G++ G +I + Sbjct: 12 GAQKAVNDLNLNFQEGSFSVLIGTSGSGKSTTLKMINRLVEHDSGEIRFAGEEIRSLPVL 71 Query: 99 ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLE-NY 157 ELR +++ QS L PH +V N A +L + ++ + + +GLE N Sbjct: 72 ELR----RRMGYAIQSIGLFPHWSVAQNIATVPQLQKWSRARIDDRIDELMALLGLESNL 127 Query: 158 AHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRT 217 YP +LSGG +QRVG+ARALA +P +LLMDE F ALDP+ R +Q E+ ++ RT Sbjct: 128 RERYPHQLSGGQQQRVGVARALAADPQVLLMDEPFGALDPVTRGALQQEMTRIHRLLGRT 187 Query: 218 IVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF----RGVDISQV 273 IV ++HD+DEA+R+ + + +M +GEVVQ G P +L PAND+VR FF GV + + Sbjct: 188 IVLVTHDIDEALRLAEHLVLMDHGEVVQQGNPLTMLTRPANDFVRQFFGRSELGVRLLSL 247 Query: 274 FSAKDIARR 282 S D RR Sbjct: 248 RSVADYVRR 256 Lambda K H 0.319 0.137 0.378 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: 295 Number of extensions: 8 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: 400 Length of database: 308 Length adjustment: 29 Effective length of query: 371 Effective length of database: 279 Effective search space: 103509 Effective search space used: 103509 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 (21.7 bits) S2: 49 (23.5 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