Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_022947842.1 H035_RS0104685 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= SwissProt::P9WQI3 (393 letters) >NCBI__GCF_000421465.1:WP_022947842.1 Length = 381 Score = 376 bits (965), Expect = e-109 Identities = 211/396 (53%), Positives = 271/396 (68%), Gaps = 28/396 (7%) Query: 1 MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60 MAEI L+ + K + DG AV++++ TI DGEF ILVGPSGCGK+T LNMI GLE IS G Sbjct: 1 MAEIQLEGITKRFADGTEAVKNVSFTIRDGEFFILVGPSGCGKSTLLNMIVGLERISEGR 60 Query: 61 LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120 L + G +N+ PKDR++AMVFQSYA+YPHMTVR+N+AFPL +AK KA+I ++V E A+ Sbjct: 61 LLLNGRCINDLDPKDRNMAMVFQSYAIYPHMTVRRNMAFPLKMAKRSKAEIERRVEEVAR 120 Query: 121 ILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQL 180 IL+LT LL+RKP+ LSGGQRQRVAMGRA+VR P+AFL+DEPLSNLDA+LRVQMR EIA+L Sbjct: 121 ILELTELLERKPANLSGGQRQRVAMGRAMVRDPEAFLLDEPLSNLDARLRVQMRTEIARL 180 Query: 181 QRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAM 240 Q++LGTT VYVTHDQTEAMTLG+R+ V+ G QQIGTP +LYERPAN FVAGFIGSP M Sbjct: 181 QKQLGTTMVYVTHDQTEAMTLGERIAVLERGEVQQIGTPRDLYERPANRFVAGFIGSPTM 240 Query: 241 NFFPARLTAIGLTLPFGEVTL-------APEVQGVIAAHPKPENVIVGVRPEHIQDAALI 293 NF PA + L LP E+ L P +QG VI G+RPEH+ Sbjct: 241 NFLPATIENGRLQLPMVELELPDCFRKHRPPIQG---------PVIAGIRPEHLLSTPPR 291 Query: 294 DAYQRIRALTFQVKVNLVESLGADKYLY--FTTESPAVHSVQLDELAEVEGESALHENQF 351 D + +F++ V LVE LGAD +++ + + H +L E+ G+S + Sbjct: 292 DK----SSPSFRLPVELVEWLGADLFVHLPLSVDRRPPHETRLPEI----GQS--FKFYL 341 Query: 352 VARVPAESKVAIGQSVELAFDTARLAVFDADSGANL 387 +AR+ A +V Q +EL +L +FD +G L Sbjct: 342 IARLDASIQVNKSQPIELWLAPDKLHLFDVHTGDRL 377 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: 440 Number of extensions: 16 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: 381 Length adjustment: 30 Effective length of query: 363 Effective length of database: 351 Effective search space: 127413 Effective search space used: 127413 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: 50 (23.9 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