Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= SwissProt::P9WQI3 (393 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 350 bits (899), Expect = e-101 Identities = 201/389 (51%), Positives = 259/389 (66%), Gaps = 42/389 (10%) Query: 1 MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60 MAEI L V KSY G + ++L IADGEF+++VGPSGCGK+T L M+AGLE+I++GE Sbjct: 1 MAEISLRDVRKSY-SGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGE 59 Query: 61 LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120 + I G VN P++RDIAMVFQ+YALYPHMTVR+N+A+ L +AK+ KA+I ++V+ +AK Sbjct: 60 IAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAK 119 Query: 121 ILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQL 180 +L+L LLDRKP QLSGGQRQRVAMGRA+VR+P AFL+DEPLSNLDAKLRVQMR +I +L Sbjct: 120 MLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKEL 179 Query: 181 QRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAM 240 QR + TT++YVTHDQ EAMTL DR+VVM G+A+QI TP E+Y+RPA FVAGFIGSPAM Sbjct: 180 QRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAM 239 Query: 241 NFFPARLTAIGLTLPFGEVTLAPEVQGVIAAHPKP--ENVIVGVRPEHIQDAALIDAYQR 298 N PAR GL G+ A EV G A P P ++I+G+RPEH+ A + Sbjct: 240 NMLPAR----GL----GD---ALEVAGQRLAVPAPAGRDLILGIRPEHLHPAGPEEP--- 285 Query: 299 IRALTFQVKVNLVESLGADKYLYFTTESPAVHSVQLDELAEVEGESALHENQFVARVPAE 358 F++ V VE LGAD + + S V R P + Sbjct: 286 ----GFELHVQAVEWLGADAFAH---------------------GSLADGTDLVLRTPGK 320 Query: 359 SKVAIGQSVELAFDTARLAVFDADSGANL 387 + V +++A D A L +FDA +G L Sbjct: 321 APVRERDRLKVAPDAAALHLFDAGTGRRL 349 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: 434 Number of extensions: 18 Number of successful extensions: 4 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: 393 Length of database: 349 Length adjustment: 30 Effective length of query: 363 Effective length of database: 319 Effective search space: 115797 Effective search space used: 115797 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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