Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= uniprot:A0A0C4YP23 (465 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 410 bits (1055), Expect = e-119 Identities = 200/450 (44%), Positives = 294/450 (65%), Gaps = 3/450 (0%) Query: 9 TDATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQL 68 T+ +L+RGL+ RHI+L+ALG AIG GLFLG A I++AGP++LL Y + G+ F IMR L Sbjct: 3 TNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRAL 62 Query: 69 GEMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIP 128 GEM V PVAGSFS +A Y G G+++GWNYW ++++ +AE++AVG+Y+ W+P +P Sbjct: 63 GEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVP 122 Query: 129 TWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTA--GPQA 186 W AL + + A+NL +VK++GE EFWF+++KV+ IV MIV GG ++ G G Sbjct: 123 QWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPT 182 Query: 187 SVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYR 246 +SNLW HGGF PNG G++MA+ ++MF++ G+E++G+TA EAD P+K+IP A N V +R Sbjct: 183 GISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWR 242 Query: 247 ILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGV 306 ILIFYVGAL V++S+YPW ++ T GSPFV+ F + A ++N VVLTAALS N G+ Sbjct: 243 ILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGI 302 Query: 307 YCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMG 366 Y RMLF LA+QG AP+ + GIP A+ VS +A V++NY +P + F + Sbjct: 303 YSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTS 362 Query: 367 LVVSALIINWAMISIIHLKFRRD-KRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLT 425 I W ++ I +K+RR A + F+ +P +Y+ LAFL ++ +M Sbjct: 363 AATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYF 422 Query: 426 PGLRISVYLIPAWLAVLGLSYRLRQKQKRA 455 P R+++ + P WL +L + Y + +RA Sbjct: 423 PDTRVALIVGPLWLVLLTVLYYVFGLGRRA 452 Lambda K H 0.326 0.140 0.426 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: 623 Number of extensions: 32 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: 465 Length of database: 454 Length adjustment: 33 Effective length of query: 432 Effective length of database: 421 Effective search space: 181872 Effective search space used: 181872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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