Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF1015 HP15_994 glycine betaine/carnitine/choline ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Marino:GFF1015 Length = 315 Score = 182 bits (463), Expect = 9e-51 Identities = 97/259 (37%), Positives = 157/259 (60%), Gaps = 10/259 (3%) Query: 32 EQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVD 91 + + + G ++ V +L +E GE+ V++G SG GKST +R++N+L+ + GQ+L+DG D Sbjct: 5 KNVTRRFGDAVAVDRINLTVETGEVCVLVGSSGCGKSTTLRMINQLLPHSEGQILVDGND 64 Query: 92 IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQ 151 + ++ +LR + V Q L PH TV N A +L E E+ + L Sbjct: 65 VTAMNPEQLR----LNMGYVIQGTGLFPHWTVARNIAMVPQLLKWPRERVDERVHELLTL 120 Query: 152 VGLE--NYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVK 209 + L+ +A+ YP +LSGG QRVG+ARALA NP+ILLMDE F ALD + R +Q E+++ Sbjct: 121 LDLDPATHANKYPQQLSGGQAQRVGVARALAANPNILLMDEPFGALDAITRENLQLEMLR 180 Query: 210 LQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF---- 265 +Q++ ++T VF++HD+DEA+R+ RIA+M G ++Q TP+ IL PA+ +V Sbjct: 181 IQSQLRKTTVFVTHDIDEALRLATRIAVMDQGRIIQHDTPENILRRPASVFVENLVGKQD 240 Query: 266 RGVDISQVFSAKDIARRTP 284 RG+ + + + +D+ P Sbjct: 241 RGLKLMSLHTVRDLMEAHP 259 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: 286 Number of extensions: 12 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: 315 Length adjustment: 29 Effective length of query: 371 Effective length of database: 286 Effective search space: 106106 Effective search space used: 106106 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