Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 200256 SO1074 tyrosine-specific transport protein, putative (NCBI ptt file)
Query= SwissProt::Q02DS7 (417 letters) >FitnessBrowser__MR1:200256 Length = 395 Score = 197 bits (500), Expect = 6e-55 Identities = 123/400 (30%), Positives = 210/400 (52%), Gaps = 13/400 (3%) Query: 15 LLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPVG 74 +LG I+AGTA+GAGM +LP+A + + ++ + ++ W + +++LE NL VG Sbjct: 5 MLGSIAIVAGTAIGAGMLALPLATAALGMVPAILLMVVIWGLSAYTSLLMLEINLRSGVG 64 Query: 75 SSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLAG 134 + IT LLG+ +V G S +L LT AY++GG S++ + + L +LA Sbjct: 65 DNVHAITGKLLGKKGQIVQGASFLSLLVALTAAYLTGGSSLLVLKAQNMFDIVLDNQLAV 124 Query: 135 LLFALAV----ALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSGEPD 190 +LF + + AL V W VD+++ + MI+ + + LL + + + S Sbjct: 125 VLFTIVLGGFAALGVAW----VDKVSRFLFSLMILLLIVVVLFLLPEVSISTIATSAVAQ 180 Query: 191 AVYWPYLLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLWQAST 250 ++ + +A +P TSFG+H + +L++Y D + + L IG+ I LA Y+ W T Sbjct: 181 SLTSSW-MAAIPVVFTSFGFHVCIATLVRYLDGDTVSLRKVLLIGSTIPLACYIFWLLVT 239 Query: 251 LGTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTLGLFD 310 LGT+ + G ++ L+ L I + ++ ++ F++LA+ +SFLGVTL L+D Sbjct: 240 LGTVGGNEINGF---NGSLPALISALQEIAHTPLISKCISLFADLALITSFLGVTLSLYD 296 Query: 311 YLADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVPALMA 370 ++A+L R + GR +T LLTFVPP + L P GF+ +GFA + + +P MA Sbjct: 297 FVAELTRAKKTFVGRAQTWLLTFVPPLLCALYVPEGFVAVLGFAAVPLVVMIIFLPIAMA 356 Query: 371 RASRKRFGSPLFRAWGGTPAIVLVLLFGVANAVAHILASL 410 R + ++ GGT A+ L + G A + +L Sbjct: 357 LRQR-QIQPQGYQVVGGTFALGLAGILGAIIIGAQLFVAL 395 Lambda K H 0.326 0.141 0.445 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: 456 Number of extensions: 22 Number of successful extensions: 3 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: 417 Length of database: 395 Length adjustment: 31 Effective length of query: 386 Effective length of database: 364 Effective search space: 140504 Effective search space used: 140504 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: 50 (23.9 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