Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= SwissProt::P9WQI3 (393 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 138 bits (347), Expect = 4e-37 Identities = 85/220 (38%), Positives = 129/220 (58%), Gaps = 8/220 (3%) Query: 1 MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60 M + L V KSY + +RD++L I DGEF+ ++G SG GKTT ++++AGL +GE Sbjct: 1 MPILELKGVAKSY-GASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGE 59 Query: 61 LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120 + + G+ V+ D +VFQSY+L P +TV NIA + A M A A++ + AK Sbjct: 60 VLLRGKPVDGPGA---DRGVVFQSYSLMPWLTVEGNIALAVD-AVMPDASKAERKARVAK 115 Query: 121 ILDLTNL---LDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEI 177 + + L +R+PS+LSGG RQRVA+ RA+ P L+DEPLS LDA R +++ EI Sbjct: 116 YIGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEI 175 Query: 178 AQLQRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIG 217 + + T + +T+D EA+ L DR++ + G G Sbjct: 176 EAIWEQEKKTVILITNDVDEALLLADRIIPLNPGPGATFG 215 Score = 132 bits (332), Expect = 2e-35 Identities = 81/219 (36%), Positives = 119/219 (54%), Gaps = 8/219 (3%) Query: 4 IVLDHVNKSYPDGH---TAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60 + V K YP T V +L + GEF+ L+G SGCGK+T L M AGL D+S G Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352 Query: 61 LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPL--TLAKMRKADIAQKVSET 118 + + G V+E P D A+VFQ+ +L+P +T QN+A + A+ VS Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYY 409 Query: 119 AKILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIA 178 + + L + +D+K S +S G RQRV + RA PK L+DEP LD+ R +++ + Sbjct: 410 LERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLM 469 Query: 179 QLQRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIG 217 ++ R T + VTHD EA+ L D+VV+M G +IG Sbjct: 470 EVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIG 508 Lambda K H 0.319 0.135 0.377 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: 508 Number of extensions: 34 Number of successful extensions: 6 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: 393 Length of database: 553 Length adjustment: 33 Effective length of query: 360 Effective length of database: 520 Effective search space: 187200 Effective search space used: 187200 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 (21.8 bits) S2: 51 (24.3 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