Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423 Length = 466 Score = 277 bits (709), Expect = 5e-79 Identities = 153/417 (36%), Positives = 233/417 (55%), Gaps = 3/417 (0%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 L +G K RH+ ++++ G IG GLF+GS + AAGP+++L Y G++ ++MR LGEM Sbjct: 13 LAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLLVVLVMRMLGEMA 72 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 P GSFS +A + G + GF GW YW +VLV E A G ++ W+P + W+ Sbjct: 73 VANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAIDAWLF 132 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQAS-ISNL 188 A V + NL +V YGE EFWFA+ KVVA+IG I G +L+ +AS +S L Sbjct: 133 ASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREASGLSRL 192 Query: 189 W-SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247 HGGF P+G + IMFSF G E + I AAE+D P ++I KA VI+RI +F Sbjct: 193 MEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWRIGVF 252 Query: 248 YICSLAVLLSLYPWNE-VAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYAN 306 Y+ S+ V++S+ PWN+ + A + + ++++VVL A S NS +Y Sbjct: 253 YLLSIFVVISVVPWNDPLLASVGSYQRALELMNIPHAKFLVDMVVLIAVASCMNSSIYIA 312 Query: 307 SRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVV 366 SRMLY L +G+AP+AL GVP A+ S + + +Y +PA L+A Sbjct: 313 SRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMPAGLFQFLLASSG 372 Query: 367 AALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTP 423 A +L + +I+++ L+ RR + L F+ + FP W+ + F++ L ++ +TP Sbjct: 373 AIALLVYLVIAISQLRMRRMLQRQNIELPFRMWLFPWLTWLVIVFISAALAVMMVTP 429 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: 486 Number of extensions: 18 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