Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 207689 DVU2205 tryptophan-specific transport protein
Query= SwissProt::Q02DS7 (417 letters) >MicrobesOnline__882:207689 Length = 425 Score = 485 bits (1248), Expect = e-141 Identities = 234/410 (57%), Positives = 309/410 (75%) Query: 7 QTPSRRPSLLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILE 66 Q + PS+LGG+MIIAGT +GAGMFSLP +G+WF +S+ V TW CM SG+MILE Sbjct: 14 QAGVKNPSVLGGAMIIAGTTIGAGMFSLPSVSAGMWFFYSLFVLFGTWLCMCHSGLMILE 73 Query: 67 ANLNYPVGSSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGV 126 ANLNYP G+SF I +D L + ++N LS+AFVLYILTYAYISGGGSI+ +T+ + +G+ Sbjct: 74 ANLNYPAGTSFDNIAKDCLARPVRLLNSLSVAFVLYILTYAYISGGGSIVAHTVKAAVGI 133 Query: 127 TLPEKLAGLLFALAVALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNS 186 +P KL G LFAL +A VVW STRAVDRI+T+MLGGMI+TF S+SGL+ +QPA+LF++ Sbjct: 134 DVPMKLGGFLFALVLAFVVWLSTRAVDRISTIMLGGMILTFFSSVSGLMFNVQPAVLFDT 193 Query: 187 GEPDAVYWPYLLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLW 246 G+ A Y P++LATLP+ LTSFGYHGNVP L+KYY KDP+ +++++ G+ + L +Y+ W Sbjct: 194 GDTSAPYSPFILATLPYFLTSFGYHGNVPGLVKYYNKDPKAVAKTIIYGSFLGLILYVCW 253 Query: 247 QASTLGTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTL 306 Q S LG IPRE+F I+A G N+G LV L ++T S +L+ LL FS+LAVA+SFLGVTL Sbjct: 254 QLSVLGNIPREEFLDIVAKGGNMGILVGALSKVTGSTNLDYLLQVFSHLAVATSFLGVTL 313 Query: 307 GLFDYLADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVP 366 GLFD +AD FDDS GR KTA++TFVPP IGGL +P+GFI AIGFAGLAA +AVIVP Sbjct: 314 GLFDCIADTLGFDDSRLGRTKTAIVTFVPPAIGGLFYPDGFIMAIGFAGLAATVFAVIVP 373 Query: 367 ALMARASRKRFGSPLFRAWGGTPAIVLVLLFGVANAVAHILASLHWLPEY 416 A+MA A+R++FG+ +RA GG + + + +G+ A+ H+L LP Y Sbjct: 374 AMMALATRRKFGNTTYRAPGGNVMLYVTIAYGITVAICHVLTMFDMLPVY 423 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: 637 Number of extensions: 26 Number of successful extensions: 2 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: 425 Length adjustment: 32 Effective length of query: 385 Effective length of database: 393 Effective search space: 151305 Effective search space used: 151305 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