Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 6938836 Sama_2939 tyrosine-specific transport protein, putative (RefSeq)
Query= SwissProt::Q02DS7 (417 letters) >FitnessBrowser__SB2B:6938836 Length = 395 Score = 213 bits (541), Expect = 1e-59 Identities = 126/397 (31%), Positives = 212/397 (53%), Gaps = 9/397 (2%) Query: 16 LGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPVGS 75 LG I+AGTA+GAGM +LP+A + + ++ + L+ W + +++LE NL VG Sbjct: 6 LGSIAIVAGTAIGAGMLALPLATAALGVIPALLLLLVVWAISAYTSLLMLEINLRSGVGD 65 Query: 76 SFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLAGL 135 + IT LG+ ++ G S +LY LT AY++GG S++ + + S + L +LA L Sbjct: 66 NVHAITGKTLGKKGQLIQGASFLSLLYALTAAYLTGGSSLLVHRMESVFSINLDGQLAVL 125 Query: 136 LFALAVALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSG--EPDAVY 193 LF L + V VD+++ L+ M++ L + LL I+P+++ + A Sbjct: 126 LFTLVLGSVAALGVSWVDKLSRLLFSLMVVLLVLVVGFLLPEIRPSVIAADAFEKVSANA 185 Query: 194 WPYLLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLWQASTLGT 253 W +A +P TSFG+H + +L++Y D + + L IG+ I L Y+LW TLGT Sbjct: 186 W---MAAIPVVFTSFGFHVCIATLVRYLDGDAVNLRKVLLIGSTIPLVCYILWLLVTLGT 242 Query: 254 IPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTLGLFDYLA 313 + ++ I + L+ L + A + + F++LA+ +SFLGVT+ LFD+LA Sbjct: 243 VGGDE---IATFNGALPKLISALQELAAHPVVGQSIAVFADLALVTSFLGVTMSLFDFLA 299 Query: 314 DLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVPALMARAS 373 ++ R GR +T ++TF+PP + L P GF+ +GFA + F + +P MA Sbjct: 300 EMTRSKGGIGGRLQTWIITFLPPLLCALFVPEGFVAVLGFAAIPLVFMIIFLPIAMALNQ 359 Query: 374 RKRFGSPLFRAWGGTPAIVLVLLFGVANAVAHILASL 410 R ++ ++ GG A+ L+ + GVA A + +L Sbjct: 360 RAQYRDG-YQVSGGKLALSLIGVAGVAIIAAQLWVAL 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: 448 Number of extensions: 17 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