Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 131 bits (329), Expect = 3e-35 Identities = 91/265 (34%), Positives = 146/265 (55%), Gaps = 14/265 (5%) Query: 5 ATAPKLAVSTTDVAIEITN--MNKWYGDFHVLRDIN---LRVMRGERIVVAGPSGSGKST 59 AT P L + + + W G ++R ++ L V GE + + G SG GKST Sbjct: 266 ATTPLLQLENVTQHFRVAQSWLQGWRGGGEIVRAVDGLSLEVWPGETLGLIGESGCGKST 325 Query: 60 MIRCINRLEEHQKGKIVVDGIELTN-DLKKIDEVRREVGMVFQH--FNLFPHLTILENCT 116 ++R I +L +GK++ G +LT +++ +RRE+ ++FQ L P LTI + Sbjct: 326 LLRTILQLLRPSQGKVLFQGQDLTQLPDRRLRSLRRELQLIFQDPAACLNPRLTI-GDAI 384 Query: 117 LAPIWVRKMPK-KEAEQVAMHFLERVKI---PEQALKYPGQLSGGQQQRVAIARSLCMRP 172 P+ ++ + + A+Q + LE+V + P +YP QLSGGQQQRVAIAR+L RP Sbjct: 385 ADPLKIQGLARGAAAKQQVLAILEQVGLTPAPTWIDRYPHQLSGGQQQRVAIARALITRP 444 Query: 173 KILLFDEPTSALDPEMVKEVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQI 231 K++L DEP S LD + +VL M L ++ +T + VTH++ AR+ +RV + +G+I Sbjct: 445 KLVLCDEPVSMLDATVQAQVLALMQELKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKI 504 Query: 232 VEQNSPAEFFDNPQHERTKLFLSQI 256 VE A+ P+H T+ L+ + Sbjct: 505 VEIGPAAQVLTQPEHPYTRSLLASL 529 Score = 116 bits (291), Expect = 9e-31 Identities = 80/231 (34%), Positives = 132/231 (57%), Gaps = 12/231 (5%) Query: 34 LRDINLRVMRGERIVVAGPSGSGKSTMIRCINRL---EEHQKGKIVVDGIELTN-DLKKI 89 L+ ++L + GER+ + G SG GKST+ R I RL HQ+G I + G L + + Sbjct: 21 LQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQQGDIRLAGQALGQLQGRSL 80 Query: 90 DEVRR-EVGMVFQH--FNLFPHLTILENCTLAPIWVRK--MPKKEAEQVAMHFLERVKIP 144 R +VG+VFQ L P TI ++ L + V + + +++A+Q A+ +LERV+IP Sbjct: 81 QRFRGGQVGLVFQDPMTRLDPLQTIGDHL-LETLQVHRPHLSRRQAKQQALSWLERVRIP 139 Query: 145 EQAL-KYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVGL-AEE 202 +YP Q SGG +QRVAIA +L ++P++++ DEPT++LD + E+L + L +EE Sbjct: 140 ANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVAAEILQELTRLCSEE 199 Query: 203 GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFL 253 +++ ++H++ +R+ + QGQ+VE PQH T+ L Sbjct: 200 NTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAVLTRPQHPYTQTLL 250 Lambda K H 0.322 0.136 0.397 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: 357 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 258 Length of database: 536 Length adjustment: 30 Effective length of query: 228 Effective length of database: 506 Effective search space: 115368 Effective search space used: 115368 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 (21.9 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