Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 7024668 Shewana3_1846 aromatic amino acid transporter (RefSeq)
Query= SwissProt::Q02DS7 (417 letters) >FitnessBrowser__ANA3:7024668 Length = 395 Score = 233 bits (593), Expect = 1e-65 Identities = 132/395 (33%), Positives = 222/395 (56%), Gaps = 12/395 (3%) Query: 17 GGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPVGSS 76 G ++IAGT +GAGM +LPIA +G+ FG S + LL W M + ++++E + P +S Sbjct: 8 GSLLLIAGTTIGAGMLALPIASAGLGFGVSSLIMLLLWALMAYTALLMVEIHQFAPSDAS 67 Query: 77 FSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLAGLL 136 + + R LLG V+ +++ F+LY L AYI+GGG + L++ LG+ LP + + Sbjct: 68 LNQLARTLLGAKGQVIASIALMFLLYALCAAYIAGGGEQVNQKLNAWLGLELPTQAGAIF 127 Query: 137 FALAVALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSGEPDAVYWPY 196 F L + +V T VD I ++ II L ++ LL +++ L + Sbjct: 128 FTLLIGTIVGLGTHCVDLINRVLFSLKIIALILMLALLLPQVEGTHLLELPLEQGL---- 183 Query: 197 LLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLWQASTLGTIPR 256 +++ +P TSFG+HG++PS+++Y G + + + + + +G+ + L IYLLWQ + G + + Sbjct: 184 IVSAIPVIFTSFGFHGSIPSVVRYLGVEVKSLRKIMLLGSALPLLIYLLWQLGSQGVLSQ 243 Query: 257 EQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTLGLFDYLADLC 316 Q + ++ + L + S L++ ++ F++LA+A+SFLGV+LGLFD++A Sbjct: 244 SQ----LMTNQSLSGFINQLASVLHSQYLSSAISVFADLALATSFLGVSLGLFDFMAANL 299 Query: 317 RFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVPALMA---RAS 373 R D+ GR TA +TFVPP L +P GFI A+G+A +A A+ +P M R + Sbjct: 300 RQQDNAAGRSITAAITFVPPLGFALFYPQGFITALGYAAIALVILAIFLPVTMVWVQRQT 359 Query: 374 RKRFGSPL-FRAWGGTPAIVLVLLFGVANAVAHIL 407 R + P +R GG ++L +L GVA A +L Sbjct: 360 RDKANLPQGYRVAGGKLGLLLAMLCGVAVIGAQLL 394 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: 434 Number of extensions: 26 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: 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