Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_052665584.1 NITAL_RS08025 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= SwissProt::P9WQI3 (393 letters) >NCBI__GCF_000969705.1:WP_052665584.1 Length = 399 Score = 360 bits (925), Expect = e-104 Identities = 207/401 (51%), Positives = 260/401 (64%), Gaps = 23/401 (5%) Query: 1 MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60 MA +V + VNK YPDG+ A+ DLNL IADGEF+ILVGPSGCGK+T L M+AGLE+I+SG+ Sbjct: 1 MANVVFEDVNKVYPDGYQAIFDLNLEIADGEFVILVGPSGCGKSTALRMVAGLEEITSGK 60 Query: 61 LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120 L I VN+ PK+RDIAMVFQSYALYPHM+V N+ F L LAK+ K +I ++V E + Sbjct: 61 LSIGDRVVNDLTPKERDIAMVFQSYALYPHMSVADNMGFALKLAKVDKKEIDRRVKEASD 120 Query: 121 ILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQL 180 IL L LDRKP LSGGQRQRVAMGRAIVR P+AFLMDEPLSNLDAKLRVQMR EIA L Sbjct: 121 ILGLDEHLDRKPKALSGGQRQRVAMGRAIVRSPQAFLMDEPLSNLDAKLRVQMRAEIAAL 180 Query: 181 QRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAM 240 Q RLG TTVYVTHDQ EAMT+GDRV V+ G Q+ P+ LY+RP NLFVAGF+GSP+M Sbjct: 181 QDRLGVTTVYVTHDQVEAMTMGDRVAVLKKGYLMQVDAPQVLYDRPDNLFVAGFMGSPSM 240 Query: 241 NFFPARLT----AIGLTLPFGEVTL-APEVQGVIAAHPKPE-----NVIVGVRPEHIQDA 290 N A + + + L GE L P+ + +PK V VG+RPEH A Sbjct: 241 NLAEAVIRKEDGKVWIELDRGENRLHVPD--AALDRYPKVAERDGGKVAVGMRPEHFAPA 298 Query: 291 ALIDAYQRIRALTFQVKVNLVESLGADKYLYFTTESPAVHSVQLDE-------LAEVEGE 343 + Q + Q +V LVE LGA+ ++F+T S + + + E +++ + Sbjct: 299 EEVGPDQ----VWKQREVTLVELLGAEMLIHFSTTSAPIVTDDMKEAMDDEEAFEDLQRQ 354 Query: 344 SALHENQFVARVPAESKVAIGQSVELAFDTARLAVFDADSG 384 +A F AR K +G ++ F T L FDA+ G Sbjct: 355 AAEGGQSFTARFEPTYKAKLGDRKDVGFQTEHLHFFDAEHG 395 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: 476 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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