Align tryptophan permease (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 201 bits (511), Expect = 5e-56 Identities = 125/396 (31%), Positives = 207/396 (52%), Gaps = 9/396 (2%) Query: 75 TSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGL 134 ++ L++ LKPRH+ M++I G IG GLFVGSG AIA GP V++ +A AG+ ++ + L Sbjct: 8 SNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGP-AVLLAYAAAGALVVLVMRML 66 Query: 135 GEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSID 194 GE+ V P G+F+ Y R + F + +Y W V+PLE AAA + W ++ Sbjct: 67 GEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVA 126 Query: 195 PVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFIG 254 + + ++ + NLF V+ +GE EF F+ +K I + GFI L ++ I G P + G Sbjct: 127 IWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLPTSQVSG 186 Query: 255 AKYWHD-PGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETDPKG--LPSAIKQVFWRI 311 + D G L NG VL ++ +S G E+ +A+ E+ G + A V WRI Sbjct: 187 VSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRI 246 Query: 312 LFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSV 371 F+L+S+ +V LVP+ + L S + ++ I IV+ V+L++V S Sbjct: 247 GLFYLVSIFIVVALVPWNDPILASVGS-----YQTVLERMGIPNAKLIVDIVVLVAVTSC 301 Query: 372 GNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVF 431 NS ++ +SR + S+ +G P + +G P +M ++ LA + + VF Sbjct: 302 LNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFANYVAPAAVF 361 Query: 432 NWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSL 467 +L+A +G +V+L I +S +R R A+G+ + Sbjct: 362 EFLLASSGAIALLVYLVIAISQLRMRKQRMARGEKI 397 Lambda K H 0.326 0.141 0.447 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: 669 Number of extensions: 25 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: 592 Length of database: 464 Length adjustment: 35 Effective length of query: 557 Effective length of database: 429 Effective search space: 238953 Effective search space used: 238953 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 (21.6 bits) S2: 52 (24.6 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