Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 597 bits (1538), Expect = e-175 Identities = 292/449 (65%), Positives = 353/449 (78%), Gaps = 9/449 (2%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 LKRGLKNRHIQLIALGGAIGTGLFLGSA V+++AGPSMILGYAI G IAFMIMRQLGEM+ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 +EPVAGSFSHFA+ YWG F GFLSGWN WVLY+LV M+EL+AVG YVHYWWP +PTWV+ Sbjct: 71 VEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWWPEIPTWVT 130 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189 A F INAINL NVK +GE EFWFAIIKVVA++ MI G YLL SG GGP+A+++NLW Sbjct: 131 AAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSGGPEATVANLW 190 Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249 +HGGFFP+G GL LA IMFSFGGLE++G TAAEAD+P+ IPKA+NQVIYRILIFY+ Sbjct: 191 THGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIFYV 250 Query: 250 CSLAVLLSLYPWNEVAA---------GGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300 +L VLLSL PW+ + A G SPFV +FS +GS + AN+LN VVLTAALSVYN Sbjct: 251 GALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFVVLTAALSVYN 310 Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360 SG Y N+RML G+AEQG+AP +L KVD+RGVP +I +SA TF V++NYL+P AL L Sbjct: 311 SGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLNYLMPQNALEL 370 Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 LM+LVVA LV+NWA+IS +HLK R+ + G+ +FK+ W+P N++ LAF+ LIL I+ Sbjct: 371 LMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLAFVVLILGIML 430 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRR 449 M PG+ VSV +P+WL+ M Y K RR Sbjct: 431 MIPGIQVSVYAIPVWLLAMLVVYMVKSRR 459 Lambda K H 0.327 0.140 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: 633 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 461 Length of database: 472 Length adjustment: 33 Effective length of query: 428 Effective length of database: 439 Effective search space: 187892 Effective search space used: 187892 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