Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 388 bits (996), Expect = e-112 Identities = 196/439 (44%), Positives = 280/439 (63%), Gaps = 5/439 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 Q GL+RGL RHI+ +ALG AIGTGLF GSAS +Q AGP+++L Y IGG +M+MR L Sbjct: 4 QSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRAL 63 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GEM + PVAGSF +A G GFL GW Y ++V +A++TA G Y+ +W+P VP Sbjct: 64 GEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDVP 123 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG----GP 181 W+ L I +NL +VK +GE EFW +++KV A++ MI G +++ G G G Sbjct: 124 RWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGGV 183 Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241 I NLW+HGGF P+G G+ AV+MF+FGG+E+IGITA EA +PQ+ IP+A+N V Sbjct: 184 ATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAVP 243 Query: 242 YRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNS 301 RIL+FY+ +LAVL+SLYPW+ + + GSPFV IFS++G A VLN+VV++AA+S NS Sbjct: 244 LRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAINS 303 Query: 302 GVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLL 361 ++ RMLYG+A Q APR V R+GVP+M + + A A V++NY++P + L+ Sbjct: 304 DIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFTLI 363 Query: 362 MALVVAALVLNWALISLTHLKSRRAMVAAG-ETLVFKSFWFPVSNWICLAFMALILVILA 420 ++ A V W +I L+ + RR M A L F ++PV+ AFM I +L Sbjct: 364 ASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVLG 423 Query: 421 MTPGLSVSVLLVPLWLVVM 439 P ++L+ +WL+++ Sbjct: 424 WFPQTRAALLVGAVWLLLL 442 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: 557 Number of extensions: 29 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: 461 Length of database: 466 Length adjustment: 33 Effective length of query: 428 Effective length of database: 433 Effective search space: 185324 Effective search space used: 185324 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