Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO356_29455 AO356_29455 amino acid transporter
Query= uniprot:Q4KIP0 (466 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29455 Length = 484 Score = 312 bits (799), Expect = 2e-89 Identities = 165/459 (35%), Positives = 267/459 (58%), Gaps = 14/459 (3%) Query: 6 KQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQL 65 +Q L+R L NRHIQL+A+GGAIGTGLF+GS ++ +G S+IL Y I G + +MR + Sbjct: 10 EQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAM 69 Query: 66 GEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEIP 125 GEM++ +F+ FA Y G F GW+YW+ + + + + VG + Q+W+P++P Sbjct: 70 GEMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVP 129 Query: 126 TWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGSGGSQ 182 W+ A + + +N++ V+ FGE EFWFAIIK++A+V +I + ++ F G Sbjct: 130 AWIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVT 189 Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242 AS+++L FPNG G +FSF G EL+G AAE P K +PKAIN + Sbjct: 190 ASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPL 249 Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302 R+++FYV ALA ++++ W ++ + S SPFV++F + G AAA I+NFVVLT Sbjct: 250 RIILFYVLALACIIAVTSWQQV---------SPSKSPFVELFLVAGFPAAAGIVNFVVLT 300 Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362 +A S NSGV+ +SRML+GLA Q +AP +L+ VP+L+L + L+ L+ VL+ ++ Sbjct: 301 SAASSANSGVFSSSRMLFGLANQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIV 360 Query: 363 PHEALELLFALVVAALMI--NWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAF 420 P V+A+++ W+ I +++ +RK E ++K + LAF Sbjct: 361 PEVMTAFTIVSTVSAILVIFTWSTILASYIAYRKKRPELHAKSAYKMPGGVPMAWFSLAF 420 Query: 421 MVMIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKK 459 + ++ ++ + P R ++ +P W + + Y L+ A+K Sbjct: 421 LGFVLCLLALRPDTRIALLVMPGWFIWLAIAYQLTDARK 459 Lambda K H 0.327 0.141 0.440 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: 670 Number of extensions: 44 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: 466 Length of database: 484 Length adjustment: 33 Effective length of query: 433 Effective length of database: 451 Effective search space: 195283 Effective search space used: 195283 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: 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