Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 166 bits (421), Expect = 7e-46 Identities = 93/248 (37%), Positives = 140/248 (56%), Gaps = 19/248 (7%) Query: 21 AFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEP 80 A + +EK + L K L I +GE+ ++G SGSGK+T++R + L P Sbjct: 4 AIRSVEKQFGRYPALNKVDLE---------IADGELLALLGPSGSGKTTLLRTIAGLEFP 54 Query: 81 TRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAG----I 136 GQVL DG D+ S A +++ VFQ +AL HMTV N AFG+++ Sbjct: 55 DAGQVLFDGQDVTYASAAA------RRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKP 108 Query: 137 AAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALD 196 + E + + L+ V LE YP +LSGG RQRV L+RALA+ P +LL+DE F ALD Sbjct: 109 SKAEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALD 168 Query: 197 PLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNP 256 +R ++ EL ++ T +F++HD +EA+ + DR+AI+ NG + Q+GTPD++ + P Sbjct: 169 ATVRKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAP 228 Query: 257 ANDYVRTF 264 +V F Sbjct: 229 ETAFVCGF 236 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: 303 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: 339 Length adjustment: 30 Effective length of query: 370 Effective length of database: 309 Effective search space: 114330 Effective search space used: 114330 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: 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