Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= uniprot:Q4KIP0 (466 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 686 bits (1770), Expect = 0.0 Identities = 327/459 (71%), Positives = 394/459 (85%) Query: 3 QTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 62 Q + GELKRGLKNRHIQLIALGGAIGTGLFLGSAGV+KSAGPSMILGYAI GFIAF+IM Sbjct: 4 QNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAFMIM 63 Query: 63 RQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWP 122 RQLGEMIVEEPVAGSFSHFAH YWGG+ GFL+GWN WVLY+LVGM+EL+AVGKYV +WWP Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWWP 123 Query: 123 EIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSGGSQ 182 EIPTWV+AA FFVL+N IN+MNVKFFGEAEFWFAIIKVVAIV MI LG Y+L SGSGG + Sbjct: 124 EIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSGGPE 183 Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242 A+V+NLW+HGGFFPNG +GL+MA+AFIMFSFGGLE++G TAAEA +P+ VIPKAINQV+Y Sbjct: 184 ATVANLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIY 243 Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302 R+LIFYVGAL VLLSL PWD L+ S++A G +Y SSPFV++FSL+GSD AA +LNFVVLT Sbjct: 244 RILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFVVLT 303 Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362 AALSVYNSG YCN+RML G+AEQGDAP +L K++K+GVP+ ++ +SA +T + VL+NYL Sbjct: 304 AALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLNYLM 363 Query: 363 PHEALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMV 422 P ALELL +LVVA L+INWA+IS +HL+FR+ + G P FKA W P NY+ LAF+V Sbjct: 364 PQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLAFVV 423 Query: 423 MIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKAS 461 +I+G+M MIPGI+ SVYAIPVW+L + Y++ ++ + Sbjct: 424 LILGIMLMIPGIQVSVYAIPVWLLAMLVVYMVKSRRQVN 462 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: 805 Number of extensions: 42 Number of successful extensions: 1 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: 472 Length adjustment: 33 Effective length of query: 433 Effective length of database: 439 Effective search space: 190087 Effective search space used: 190087 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