Align tryptophan permease (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 184 bits (468), Expect = 5e-51 Identities = 119/401 (29%), Positives = 200/401 (49%), Gaps = 25/401 (6%) Query: 77 NLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGE 136 +L+R L+ RH+ ++A+G +IG GLF+GS AI GP +++ + + G I + LGE Sbjct: 6 SLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGP-AILLSYLLGGVAIFIIMRALGE 64 Query: 137 ITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPV 196 + V+ PV G+F+ Y +L P ++ Y W EI A + + W + Sbjct: 65 MAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQW 124 Query: 197 IWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEF-IG- 254 IW + ++NL V+ +GE EF F+ IK +T+ V++I GGG F +G Sbjct: 125 IWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTI-------VLMIVGGGAMIVFGLGN 177 Query: 255 -------AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIK 305 + W G + NG G+L L + ++ G+EM L +GE D K +P AI Sbjct: 178 QGVPTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAIN 237 Query: 306 QVFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVIL 365 VFWRIL F++ +L ++ + P+ N LG SPFV+ + IK+ I+N V+L Sbjct: 238 SVFWRILIFYVGALFVIMSIYPW---NELG---THGSPFVMTFERLGIKSAAGIINFVVL 291 Query: 366 ISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSG 425 + LS N I+++ R L ++A QG P F +G P ++ + + L L+ Sbjct: 292 TAALSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYL 351 Query: 426 SMSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKS 466 ++VF W+ + A W + ++ +++R + +S Sbjct: 352 VPAKVFVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRS 392 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: 713 Number of extensions: 46 Number of successful extensions: 5 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: 454 Length adjustment: 35 Effective length of query: 557 Effective length of database: 419 Effective search space: 233383 Effective search space used: 233383 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