Align MFS transporter (characterized, see rationale)
to candidate Echvi_2841 Echvi_2841 Major Facilitator Superfamily.
Query= uniprot:A0A1X9ZCC9 (458 letters) >FitnessBrowser__Cola:Echvi_2841 Length = 451 Score = 386 bits (991), Expect = e-112 Identities = 198/438 (45%), Positives = 282/438 (64%), Gaps = 15/438 (3%) Query: 8 ENPKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQ 67 E KL+ QI NMS GF GIQ G+ LQ AN RI + GA+ + + L +L AP+TG+++Q Sbjct: 6 EKKKLSFWQIWNMSFGFLGIQMGFALQNANASRILQTFGADVEHLSLFWLVAPITGMIIQ 65 Query: 68 PIIGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHSSV-------LWMAAGLLWILD 120 PIIG+ SDRTW K GRRRPYF+ GA++++I L+ MP++S+ LW+ AG L I+D Sbjct: 66 PIIGHYSDRTW-TKLGRRRPYFLAGAVLAAIGLVLMPNASLFVAYLPALWVGAGFLMIMD 124 Query: 121 VFGNIAMEPFRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAEQ 180 N+AMEPFRA V DKLP Q GF +Q+++IGLG + S LP+++ F + TA + Sbjct: 125 ASFNVAMEPFRALVADKLPTDQRTLGFAVQTLLIGLGAVIGSWLPYVLTEWFSIPTTANE 184 Query: 181 GSIPENVKFSFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREIFHA 240 G +P+NV ++F IGA A++LWTV T EYPP +++ + + +K G IF Sbjct: 185 GIVPQNVLWAFIIGATILVASILWTVLRTSEYPPDELE--KSAHKIDKNAQRGLSSIFTD 242 Query: 241 LRNMPKRMQIVSLVQFFTWPGLFLMWFYYTTAVAVNVFG--GKDAADPVYAQGADFGSLT 298 MPK M+ + LVQFF+W LF MW + T A+A +V+G D + + + ++ + Sbjct: 243 FIKMPKTMKQLGLVQFFSWFALFSMWVFSTPALAQHVWGLPSSDRSSLEFNEAGNYVGVI 302 Query: 299 LAYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISVAWVHDKNM---LYLCMTG 355 Y++++ LFA+ LP IA +GRK THA+CL+ G GLIS+ WV D M L L M G Sbjct: 303 FGVYNLVSALFAMTLPVIAAKIGRKMTHAICLLIGGTGLISILWVTDPEMKWVLNLSMIG 362 Query: 356 VGIAWASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRL 415 VGIAWASIL+MPYA+L+GS+P K+G+YMGIFNFFI P+I+ GW++R + + Sbjct: 363 VGIAWASILAMPYAILAGSIPAKKMGVYMGIFNFFITAPQILNGFIGGWIVRYIYGGQAI 422 Query: 416 LAVQLGGGLMILAAVICY 433 A+ G +ILAA++ Y Sbjct: 423 YALFSAGLFLILAAMLTY 440 Lambda K H 0.327 0.142 0.448 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: 724 Number of extensions: 46 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: 458 Length of database: 451 Length adjustment: 33 Effective length of query: 425 Effective length of database: 418 Effective search space: 177650 Effective search space used: 177650 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 (21.7 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