Align KguT (characterized, see rationale)
to candidate Pf6N2E2_1312 4-hydroxyphenylacetate symporter, major facilitator superfamily (MFS)
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1312 Length = 434 Score = 200 bits (508), Expect = 8e-56 Identities = 126/423 (29%), Positives = 205/423 (48%), Gaps = 19/423 (4%) Query: 4 DRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYF 63 DR W +MP++ + Y A+LDR N GFA M+ DL + + LFF+ Y Sbjct: 16 DRTHATITWRLMPLLLVCYLFAHLDRINIGFAKMQ-MSADLQFSDTVYGFGAGLFFIAYA 74 Query: 64 FFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAM 123 F VP + ++ ++ I +++WG L++ ++ S + +RFLLGV EA P + Sbjct: 75 LFGVPSNMALDRVGPRRWIATLMVVWGALSSGMFLIDSAAGFYVLRFLLGVAEAGFFPGI 134 Query: 124 LIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHF-------DWRWMFIIEGL 176 L++L W+ R++ + P+ + +SG +++HF W+WMF+IEGL Sbjct: 135 LVFLNRWYPARRRAQVTALFAIAVPMAGVIGGPLSGGILEHFHDVGGLRGWQWMFVIEGL 194 Query: 177 PAVLWAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIIL 236 P +L + + + D E WL K LRE L+ E+Q K + ++ +P+V +L Sbjct: 195 PVILLGLVVLKCLPDDFETVKWLTPHAKQQLREQLSLEEQR-KSITSFSAILNNPQVWLL 253 Query: 237 SLQYFCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQK 296 YF + V W+P+++ A G LSAVPYL M+G +SDR ++ Sbjct: 254 VAVYFAVMLAVNTLAFWMPTLIHGAGIGSDGKVGLLSAVPYLAGCFFMIGCGRSSDRHRE 313 Query: 297 RKRFVWPPLLIAALAFYGSYILGTEHFWWSYTL--LVIAGACMYAPYGPFFAIVPELLPS 354 R+ + PLL+AAL G + G L L++AG A F+ + P L + Sbjct: 314 RRWHLCVPLLMAAL---GIAVTGLSPGNPILVLSGLIVAGMGASAALPMFWQLPPAFLSN 370 Query: 355 NVAGGAMALINSMGALGSFSGSWLVGYLNGVTGGP-----GASYLFMCGALLVAVALTAV 409 +ALI+S G++ SF +L+G++ T + L G LLV A+ Sbjct: 371 GTQAAGIALISSFGSIASFFAPYLIGWMRDTTQSASLALYALALLIALGGLLVLRTHAAI 430 Query: 410 LNP 412 +NP Sbjct: 431 VNP 433 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: 584 Number of extensions: 29 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: 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