Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate BWI76_RS17620 BWI76_RS17620 ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Koxy:BWI76_RS17620 Length = 362 Score = 181 bits (459), Expect = 3e-50 Identities = 99/223 (44%), Positives = 149/223 (66%), Gaps = 6/223 (2%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 ++ SL I GE+ +G SG GK+T++R++N+L P G V + GV K++ A++ +V Sbjct: 19 IRGLSLVINSGELCTFVGPSGCGKTTILRMINQLDVPDAGDVYVQGV---KLAAADIIQV 75 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLE-NYAHAYP 162 RR+ I V QS AL PH TV N A L G + + + + + + + L+ N YP Sbjct: 76 RRQ-IGFVMQSAALFPHRTVAQNIATVPRLLGWSKKHIQARIDELVDLMSLDRNVLPRYP 134 Query: 163 DELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFIS 222 +LSGG + RV +ARALA +P +LLMDE F+A+DP++R +QDEL+ LQ + ++TIV ++ Sbjct: 135 HQLSGGQQGRVAIARALAADPPVLLMDEPFAAIDPVVRERLQDELLLLQQRLRKTIVLVT 194 Query: 223 HDLDEAMRIGDRIAIMQ-NGEVVQVGTPDEILNNPANDYVRTF 264 HD++EA+R+GDRIAI Q GE+ Q TPD IL++PA+D+VR F Sbjct: 195 HDINEAIRLGDRIAIFQEGGELAQFATPDHILSHPASDFVRRF 237 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: 381 Number of extensions: 18 Number of successful extensions: 4 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: 362 Length adjustment: 30 Effective length of query: 370 Effective length of database: 332 Effective search space: 122840 Effective search space used: 122840 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