Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 173 bits (439), Expect = 6e-48 Identities = 91/226 (40%), Positives = 135/226 (59%), Gaps = 6/226 (2%) Query: 39 GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98 G + V+ +L++E+GE ++G SG GK+T ++++ T G++ + G DI Sbjct: 14 GSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRIELAGRDITHA--- 70 Query: 99 ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYA 158 + + + +VFQS+AL PHMTV DN +FG+E+ + ER+++ AL V LE +A Sbjct: 71 ---KANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGLVHLEKHA 127 Query: 159 HSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTI 218 YP ELSGG RQRV LARAL I P +LL+DE S LD +R EMQ EL ++Q K T Sbjct: 128 GRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQRKVGTTT 187 Query: 219 VFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 V ++HD EAM I DR+ +M+ G Q+ P + +P ++ TF Sbjct: 188 VMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTF 233 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: 287 Number of extensions: 20 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: 362 Length adjustment: 30 Effective length of query: 370 Effective length of database: 332 Effective search space: 122840 Effective search space used: 122840 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