Align KguT (characterized, see rationale)
to candidate HSERO_RS22270 HSERO_RS22270 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__HerbieS:HSERO_RS22270 Length = 445 Score = 204 bits (520), Expect = 3e-57 Identities = 135/410 (32%), Positives = 210/410 (51%), Gaps = 13/410 (3%) Query: 14 IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73 ++P + + Y ++YLDR N GFAA + M DL +TP+ L LFF+GYFFF++P + Sbjct: 31 LIPFILLCYVVSYLDRINVGFAALT-MNKDLGLTPSQFGLGAGLFFIGYFFFEIPSNLAL 89 Query: 74 EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133 + + I +I WG ++ T V RFLLG+ EA P + +Y WF Sbjct: 90 HRFGARMWISRIMISWGLISMATAFVVGPKSFALARFLLGMAEAGFTPGIYLYFTQWFPG 149 Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVK------HFDWRWMFIIEGLPAVLWAFIWWR 187 A R +A F ++G PV + S +SG L++ W+ + ++E LPAVL + Sbjct: 150 AWRGKATAFFLIGIPVANIIGSPLSGALMELHGMWGFKGWQVLLLLEALPAVLLGVMCLF 209 Query: 188 LVDDRPEQASWLKAQEKTALREALAAEQQ--GIKPVKNYREAFRSPKVIILSLQYFCWSI 245 L+ DRP +A WL A EK L L+ EQ + ++AF + +V L+ FC I Sbjct: 210 LLPDRPAKAKWLSADEKQWLENELSTEQNVLAARHGNKLKDAFTNWRVFALAGANFCGII 269 Query: 246 GVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305 G LWLP I+++ L G ++A+PYL +AM + ++R ++R FV + Sbjct: 270 GSLSIGLWLPQIIRE-FGLPSHQVGLVAAIPYLVGAVAMTLWARLANRSERRLFFVAGAI 328 Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365 ++AAL+ S L T + +A A + + F+AI L A G +ALI Sbjct: 329 VLAALSLGISAFLHTPLL--KMLAITVAVASILSFQATFWAIPSGFLTGRAAAGGLALIV 386 Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVL-NPSQ 414 S+G LG F G ++G++ T G +F+ GALL+ +T L +PS+ Sbjct: 387 SIGNLGGFVGPSVIGFIREATQGFTYPLIFVAGALLLGAVITLALGDPSR 436 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: 599 Number of extensions: 37 Number of successful extensions: 6 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: 445 Length adjustment: 32 Effective length of query: 393 Effective length of database: 413 Effective search space: 162309 Effective search space used: 162309 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