Align tryptophan permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 214 bits (546), Expect = 5e-60 Identities = 144/463 (31%), Positives = 227/463 (49%), Gaps = 20/463 (4%) Query: 76 SNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLG 135 + K+ ++ RH++M+A+GG IGTGLF+ SG + + GP+G VI + I + + LG Sbjct: 12 AGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLG 71 Query: 136 EITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDP 195 E+ V+ P G+F+ Y TRFL P + V+ +Y L W + E AA + + W Sbjct: 72 ELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPV 131 Query: 196 VIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG--GGPDHEFI 253 IW A+F V+ N+ VR F E EF S IK +TV F+++ I G I Sbjct: 132 WIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAHSI 191 Query: 254 GAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVFWRI 311 G + G GF + L+ S++ G E+ +A+GET DP + +P AI+ R+ Sbjct: 192 GLSNFTREGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRL 251 Query: 312 LFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSV 371 FF+ ++ ++ L+P L+ SPFV I I+N VI+ ++LS Sbjct: 252 AVFFVGTIFVLATLLPREQAGLV------ESPFVTVFTYIGIPYSADIMNFVIISALLSA 305 Query: 372 GNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVF 431 NS ++A+SR L +++ QG +P F + R G PL I+ + G + L + ++ Sbjct: 306 ANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIY 365 Query: 432 NWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIWGSAYSALINCLI 491 L++I+GLA +VW+SI S I FR A G + +L+F W + Sbjct: 366 LALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPW----------VP 415 Query: 492 LIAQFYCSLWPIGGWTSGKERAKIFFQNYLCALIMLFIFIVHK 534 L A CSL IG ++R ++F A +I K Sbjct: 416 LGALVCCSLACIGIAFDPEQRVALYFGLPFIAWCYFVYYITRK 458 Lambda K H 0.326 0.141 0.447 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: 701 Number of extensions: 35 Number of successful extensions: 4 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: 592 Length of database: 476 Length adjustment: 35 Effective length of query: 557 Effective length of database: 441 Effective search space: 245637 Effective search space used: 245637 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 (21.6 bits) S2: 52 (24.6 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