Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 185 bits (469), Expect = 2e-51 Identities = 101/261 (38%), Positives = 151/261 (57%), Gaps = 10/261 (3%) Query: 32 EQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVD 91 E + ++ G V + SL + EGE F ++G SG GK+T++R+L PT G++LIDG D Sbjct: 18 ENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILIDGQD 77 Query: 92 IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQ 151 I+ + ++ + MVFQS+A+ PHMTV DN A+G+++ + ER + +AL Sbjct: 78 ISNVPP------NKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALEL 131 Query: 152 VGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQ 211 V L PD+LSGG RQRV LARAL P +LL+DE SALD +R +M+ EL LQ Sbjct: 132 VQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQ 191 Query: 212 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS 271 K T + ++HD DEA+ + R A+M G + QV TP ++ P + +V F V++ Sbjct: 192 EKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQVNLF 251 Query: 272 QVFSAKDIARRTPNGLIRKTP 292 + A D P+ + K+P Sbjct: 252 EGVLAVD----EPSHAVIKSP 268 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: 342 Number of extensions: 18 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: 381 Length adjustment: 31 Effective length of query: 369 Effective length of database: 350 Effective search space: 129150 Effective search space used: 129150 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: 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