Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_245300279.1 B1812_RS18275 sulfate/molybdate ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_002117405.1:WP_245300279.1 Length = 353 Score = 167 bits (423), Expect = 4e-46 Identities = 89/225 (39%), Positives = 139/225 (61%), Gaps = 10/225 (4%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 ++D SL I GE+ ++G SGSGK+T++R++ L P RG V D ++ +S V Sbjct: 14 LRDVSLDIAGGELVALLGPSGSGKTTLLRVIAGLNSPHRGAVFFDALNATSLS------V 67 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQE-RRE---KALDALRQVGLENYAH 159 + +++ VFQ++AL HM+V DN AFG++ A++ +RE + + L V LE Sbjct: 68 QERRVGFVFQNYALFKHMSVADNVAFGLKARPRASRPPKREIAARVAELLELVQLEGLGQ 127 Query: 160 AYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIV 219 YP +LSGG RQRV LARALAI P +LL+DE F ALD +R +++ L ++ + T V Sbjct: 128 RYPAQLSGGQRQRVALARALAIEPRVLLLDEPFGALDARVRKDLRRWLREIHKRTGLTTV 187 Query: 220 FISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 F++HD DEAM + DR+ ++ G + Q G+P + + PA+ +V +F Sbjct: 188 FVTHDQDEAMELADRVVVLNQGRIEQAGSPAALYDRPASAFVLSF 232 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: 321 Number of extensions: 20 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: 353 Length adjustment: 30 Effective length of query: 370 Effective length of database: 323 Effective search space: 119510 Effective search space used: 119510 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