Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_085634730.1 MGEO_RS00445 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_002115805.1:WP_085634730.1 Length = 370 Score = 350 bits (899), Expect = e-101 Identities = 191/371 (51%), Positives = 249/371 (67%), Gaps = 9/371 (2%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M L++ N K+YGA + L +++S++EG+FL+LVGPSGCGKSTL+N IAGLE IT G Sbjct: 1 MGFLDIDNTTKSYGA--VEVLHKVDISVEEGKFLVLVGPSGCGKSTLLNMIAGLEDITSG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I I D ++G+ P R+IAMVFQSYALYP M+V +NI FGL++ P+A+ + + VA Sbjct: 59 EIRIKDVVMNGVHPSKRNIAMVFQSYALYPNMTVGQNITFGLEMHGTPKAEREKAMHDVA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 KLLQIE LL+RKPG LSGGQ+QRVAMGRAL R P ++LFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 KLLQIEQLLDRKPGALSGGQRQRVAMGRALVRNPDVFLFDEPLSNLDAKLRVDMRTEIKK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +HQ L TT VYVTHDQIEAMTL ++AVM G +QQ GTP+EIY+ PAN FVA+F+GSP Sbjct: 179 LHQNLGTTIVYVTHDQIEAMTLSTRIAVMNGGYVQQLGTPQEIYDTPANIFVATFMGSPA 238 Query: 241 MNFVPLRLQRKDGR---LVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIM---LA 294 MN VP ++ +GR VAL D A + + A E RD++LG+RPE I A Sbjct: 239 MNVVPATVRLANGRPVAEVALHDGSLAELPFSQDNL-AAWEGRDILLGIRPETITDEDAA 297 Query: 295 AGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKV 354 + + + + + VTEP G DT V + L V R+ D + G T + K Sbjct: 298 DRKSSNIAHLTNRIVVTEPAGSDTFVSMTLGGKDVIARMRSDAEVRPGADFTFAVNMEKA 357 Query: 355 LLFDANTGERL 365 + FD + R+ Sbjct: 358 VAFDPASKNRI 368 Lambda K H 0.318 0.135 0.382 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: 406 Number of extensions: 15 Number of successful extensions: 3 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: 386 Length of database: 370 Length adjustment: 30 Effective length of query: 356 Effective length of database: 340 Effective search space: 121040 Effective search space used: 121040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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