Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 203671 SO4601 tryptophan-specific transport protein (NCBI ptt file)
Query= SwissProt::Q02DS7 (417 letters) >FitnessBrowser__MR1:203671 Length = 414 Score = 479 bits (1233), Expect = e-140 Identities = 246/406 (60%), Positives = 308/406 (75%), Gaps = 7/406 (1%) Query: 14 SLLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPV 73 SLLGG+MIIAGT VGAGMFSLP+ SG+WFG+S+ + L WFCML+SG+++LE NL++ Sbjct: 12 SLLGGAMIIAGTTVGAGMFSLPVVGSGMWFGYSILMLLGIWFCMLMSGLLLLETNLHFEP 71 Query: 74 GSSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLA 133 G+SF T+T++ LGQ W +VNG+SIAFVLYILTYAYISGGGSI+ ++L G+G+ LP+ +A Sbjct: 72 GASFDTLTKETLGQFWRIVNGVSIAFVLYILTYAYISGGGSIVNHSLQ-GMGIELPQSVA 130 Query: 134 GLLFALAVALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSGEPDAV- 192 GL+F + +A +V ST+AVDRITT+MLGGMIITF L+I LL I L EPD Sbjct: 131 GLVFTVVLACIVLISTKAVDRITTIMLGGMIITFFLAIGNLLIEIDVTKLL---EPDGNQ 187 Query: 193 -YWPYLLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLWQASTL 251 + PYL LPF L SFGYHGNVPSL+KYYGKD I +++++GT IAL IY+ W +T+ Sbjct: 188 RFIPYLWVALPFGLASFGYHGNVPSLVKYYGKDSSTIIKAIFVGTFIALIIYVCWLVATM 247 Query: 252 GTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTLGLFDY 311 G IPR QF IIA G N+G LV L ++ S LN++LT F+NLAVASSFLGVTLGLFDY Sbjct: 248 GNIPRSQFSEIIAQGGNMGVLVGALSKVMESSWLNSMLTLFANLAVASSFLGVTLGLFDY 307 Query: 312 LADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVPALMAR 371 LADL FDDS GR KTA++TFVPPT+ GLLFP+GF+ AIGFA LAA WAVIVPALMA Sbjct: 308 LADLFGFDDSRSGRMKTAIVTFVPPTVFGLLFPDGFLIAIGFAALAATVWAVIVPALMAY 367 Query: 372 ASRKRFGSPL-FRAWGGTPAIVLVLLFGVANAVAHILASLHWLPEY 416 SR+ F + FR +GGTP I+LV+LFGV H+LA + LP++ Sbjct: 368 KSRQLFPNHQGFRVFGGTPLIILVVLFGVVTGACHLLAMANLLPQF 413 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: 618 Number of extensions: 28 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: 417 Length of database: 414 Length adjustment: 31 Effective length of query: 386 Effective length of database: 383 Effective search space: 147838 Effective search space used: 147838 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