Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate SMc00771 SMc00771 putrescine ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Smeli:SMc00771 Length = 381 Score = 191 bits (484), Expect = 4e-53 Identities = 117/289 (40%), Positives = 172/289 (59%), Gaps = 15/289 (5%) Query: 29 LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88 +S + + +K G V D SL I E F ++G SG GKST++R+L +PT G++++D Sbjct: 24 ISVKNVTKKFGDFTAVDDLSLNIYTREFFALLGASGCGKSTLLRMLAGFEQPTSGEIILD 83 Query: 89 GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDA 148 G +A I R+ + M+FQS+AL PHMTV +N AFG++ G+ + E+ Sbjct: 84 GQSLAGIPPY------RRPVNMMFQSYALFPHMTVENNVAFGLKQDGMPKADIAERVAQM 137 Query: 149 LRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208 L+ V LE +A P +LSGG RQRV LAR+LA P +LL+DE ALD +R E Q EL+ Sbjct: 138 LKLVKLEKFAKRKPHQLSGGQRQRVALARSLAKRPKVLLLDEPLGALDKKLREETQFELM 197 Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268 LQ + T V ++HD +EAM + DRIA+M +G+VVQV TP EI P + +V F V Sbjct: 198 DLQQELGLTFVVVTHDQEEAMTMADRIAVMSHGKVVQVATPAEIYEAPNSRFVADFIGDV 257 Query: 269 DI--SQVFSAKD--IARRTPNGL-IR----KTPGFGPRSALKLLQDEDR 308 +I +V SA+D I T G+ +R + PG G ++A+ + ++ R Sbjct: 258 NIFDGKVTSAEDGYIRVETTGGIPVRMASPEKPGNGAKAAVAIRPEKIR 306 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: 327 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: 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