Align KguT (characterized, see rationale)
to candidate RR42_RS04270 RR42_RS04270 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS04270 Length = 434 Score = 212 bits (539), Expect = 2e-59 Identities = 128/407 (31%), Positives = 210/407 (51%), Gaps = 22/407 (5%) Query: 14 IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73 ++P + + Y +AYLDR N GFA M DL + + L +FF+GYF F+VP + Sbjct: 27 LVPFLLLCYVVAYLDRVNVGFAKLQ-MLGDLKFSETIYGLGAGIFFIGYFLFEVPSNVIL 85 Query: 74 EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133 K + I +I WG ++ V + ++ +RFLLG+ EA P +++YL +W+ Sbjct: 86 HKVGARIWIARIMITWGVISAAMMFVTTPTMFYVLRFLLGIAEAGFFPGIILYLTYWYPS 145 Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAFIWW 186 R R TF + ++ + +SG++++ FD W+WMF++EG+P+VL + Sbjct: 146 HRRGRTTTFFMTAIALSGVIGGPLSGWMMQSFDGRNGWSGWQWMFLLEGIPSVLVGLVVL 205 Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSIG 246 +DDR A WL +EK L+ +AAE K + SP+V ++S YF + +G Sbjct: 206 AYLDDRIVHAKWLSNEEKALLQRNIAAEDMH-KEDAPIGKVLSSPRVWLMSAIYFSFVMG 264 Query: 247 VYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPLL 306 +YG WLP+I+KQ + G L+A+PY AV M+ V++++DR ++R+ + P L Sbjct: 265 LYGVSFWLPTIIKQTGVKSPLDIGLLTAIPYGCAVAGMVLVAYSADRTRERRWHIAIPAL 324 Query: 307 IAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-----PFFAIVP-ELLPSNVAGGA 360 + A+ +L + W + T+L + G + A G P F +P L A Sbjct: 325 LGAVGL----VLSVQ--WHNNTVLALLGLTL-ATIGILTTLPLFWSLPTAFLAGTGAAAG 377 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALT 407 +ALINS+G L F + VG+L +T + + L+ ALT Sbjct: 378 IALINSLGNLAGFISPYAVGWLKDMTQSTDSGMYLLAACLVAGAALT 424 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: 625 Number of extensions: 38 Number of successful extensions: 5 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: 425 Length of database: 434 Length adjustment: 32 Effective length of query: 393 Effective length of database: 402 Effective search space: 157986 Effective search space used: 157986 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