Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_085770045.1 B1812_RS01630 ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_002117405.1:WP_085770045.1 Length = 352 Score = 168 bits (426), Expect = 2e-46 Identities = 98/285 (34%), Positives = 160/285 (56%), Gaps = 11/285 (3%) Query: 29 LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88 L+ E+ ++ G ++ + D S+ + GE F ++G SG GK+T++RL+ P G++ ++ Sbjct: 7 LAIERASKRFGSTVALDDVSVDVAPGEFFALLGPSGCGKTTLMRLIAGFERPDSGRLTLE 66 Query: 89 GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDA 148 G D+A + ++ I M+FQS+AL PH+ V +N AFG+ G+A + +++ + Sbjct: 67 GRDLAGLPP------HQRPINMMFQSYALFPHLDVFENIAFGLRRKGLAQDDVKKRVQEL 120 Query: 149 LRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208 L V L + +LSGG +QRV LARALA P +LL+DE ALD +R E Q +L Sbjct: 121 LDVVQLGGFNARRIHQLSGGQKQRVALARALAPGPKLLLLDEPLGALDRKLREETQLQLK 180 Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268 ++Q K V ++HD DEA+ + DRIA+M+ G++ Q+G P ++ P N +V F Sbjct: 181 QIQRKLNTAFVIVTHDQDEALALADRIAVMRAGKIEQIGAPPDVYRRPQNRFVADFIGAT 240 Query: 269 DI--SQVFSAKDIARRSPVGLIRK---TPGFGPRSALKLLQDEDR 308 ++ V A + +P G I + T G R+AL L + R Sbjct: 241 NLIEGHVSRADGVWFVAPFGKIARAVCTLDDGARAALSLRPQDIR 285 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: 301 Number of extensions: 13 Number of successful extensions: 2 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: 352 Length adjustment: 30 Effective length of query: 370 Effective length of database: 322 Effective search space: 119140 Effective search space used: 119140 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 Apr 09 2024. 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