Align KguT (characterized, see rationale)
to candidate RR42_RS26290 RR42_RS26290 MFS transporter permease
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS26290 Length = 439 Score = 205 bits (522), Expect = 2e-57 Identities = 123/403 (30%), Positives = 196/403 (48%), Gaps = 9/403 (2%) Query: 12 WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71 W ++P + + Y +AYLDR N GFA M DL + + L LFF+GYFFF+VP + Sbjct: 29 WRLLPFLMLCYVVAYLDRVNVGFAKLH-MLGDLQFSESAYGLGAGLFFIGYFFFEVPSNV 87 Query: 72 YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131 + K I +I+W ++ VQ+ + +RFLLG EA P M++YL +WF Sbjct: 88 LMHRIGAKATISRIMIMWSVISAAMVFVQTTTQFYVLRFLLGAAEAGFYPGMILYLTYWF 147 Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAFI 184 R+R + PV+ ++ +SG++++ W+WMF+IE LP++L Sbjct: 148 PSHRRARMVALFMCAIPVSGIFGGPLSGFIMESMQGVAGLRGWQWMFLIEALPSLLVGVA 207 Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244 +D+ A WL EK L +A E R+ F ++I ++ FC Sbjct: 208 VLAYLDNSIRSARWLTQSEKDLLERNIANENATKGGHMTMRQLFSDRRIIKMACICFCTV 267 Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304 +G YG WLPS+++QA + G L+A+P+ AV +M+ VS +SDRM++R+ + P Sbjct: 268 MGQYGLTFWLPSLIRQAGVSGALHIGLLTAIPFSVAVCSMILVSRSSDRMRERRWHLIVP 327 Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALI 364 A S I +++ S L +A A F+++ LL A +A+I Sbjct: 328 FCCGAAGLALSAIF-SDNVVLSLAALALAAGGSLATSPLFWSLPTALLSGAGAAAGIAMI 386 Query: 365 NSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALT 407 NS L F +++G + T + + G LL ALT Sbjct: 387 NSFANLAGFVSPYMIGLIKDATQSTNLAMFVLAGVLLCGAALT 429 Lambda K H 0.328 0.140 0.457 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: 557 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 439 Length adjustment: 32 Effective length of query: 393 Effective length of database: 407 Effective search space: 159951 Effective search space used: 159951 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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