Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Ac3H11_631 Methionine ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_631 Length = 351 Score = 175 bits (443), Expect = 2e-48 Identities = 100/274 (36%), Positives = 158/274 (57%), Gaps = 3/274 (1%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 ++ L I+ GE+F I+G SG+GKS++VR++N L PT GQV++ G D+ +++DA+LRE Sbjct: 21 LRGIDLTIQPGEVFGIIGKSGAGKSSLVRVINLLNRPTTGQVIVGGRDLTQLNDAQLREA 80 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163 RR+ I MVFQ F L+ TV DN A +ELAG++ + RE+ L VGL++ A YP Sbjct: 81 RRE-IGMVFQHFNLLSSRTVFDNAALPLELAGMSKTDIRERVNPLLELVGLDHLADRYPA 139 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 ++SGG +QRVG+ARALA P +LL DEA SALDP + D L ++ + T+V I+H Sbjct: 140 QISGGQKQRVGIARALASRPKVLLSDEATSALDPETTRSILDLLRQVNRELGLTVVLITH 199 Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQV-FSAKDIARR 282 + ++ D +A+++ G +V+ G ++ P ++ + ++ S D R+ Sbjct: 200 QMQVIKQVADHVAVIEAGRIVEQGRVLDVFTRPQQAITKSLIDEILPQELPVSVLDHVRK 259 Query: 283 TPNGLIRKTPGFGPRSALKLLQDEDREYGYVIER 316 L P R L+L D Y ++ + Sbjct: 260 LTRQLATTAPDHAGR-LLRLSYSGDSAYQPILSQ 292 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: 339 Number of extensions: 15 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: 351 Length adjustment: 30 Effective length of query: 370 Effective length of database: 321 Effective search space: 118770 Effective search space used: 118770 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