Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__psRCH2:GFF4241 Length = 335 Score = 172 bits (435), Expect = 2e-47 Identities = 95/249 (38%), Positives = 146/249 (58%), Gaps = 2/249 (0%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 ++ L I GE+F ++G SG+GKST++RL+NRL EP+ G++L++G D+ + LR Sbjct: 21 LQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNGEDVTALDADGLRRF 80 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDAL-RQVGLENYAHSYP 162 R++ + M+FQ F L+ TV DN A + LAGI + + + AL +VGL+ +A YP Sbjct: 81 RQR-VGMIFQHFNLLMSKTVADNVAMPLRLAGIRSRREIDARVAALLERVGLKEHARKYP 139 Query: 163 DELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFIS 222 +LSGG +QRVG+ARALA P ILL DEA SALDP + L ++ + + TIV I+ Sbjct: 140 AQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLIT 199 Query: 223 HDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARR 282 H++D R+ DR+A+M G +V+ G E+ +P + + F + D Sbjct: 200 HEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKHPTTQRFVLEDEAMDESELHDDFAH 259 Query: 283 TPNGLIRKT 291 P ++R T Sbjct: 260 VPGRILRLT 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: 313 Number of extensions: 17 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: 335 Length adjustment: 30 Effective length of query: 370 Effective length of database: 305 Effective search space: 112850 Effective search space used: 112850 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: 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