Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= uniprot:Q4KIP0 (466 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 737 bits (1903), Expect = 0.0 Identities = 358/452 (79%), Positives = 403/452 (89%) Query: 3 QTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 62 +TL G L+RGLKNRHIQLIALGGAIGTGLFLGSAGVL+SAGPSMILGYAI GFIAFLIM Sbjct: 4 ETLHTGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIM 63 Query: 63 RQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWP 122 RQLGEMIVEEPVAGSFSHFAHKY GGY GFL+GWNYWVLYVLVGMAELTAVGKYVQFWWP Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWP 123 Query: 123 EIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSGGSQ 182 E+PTW +AA FFVL+NLIN+ NVK FGE EFWFAI+KV AIVGMI+LG ++L SG GG Q Sbjct: 124 EVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKGGEQ 183 Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242 AS+SNLWSHGGFFPNG +G+L+A+A IMFSFGGLELVGITAAEAAEP+ VIPKAINQVVY Sbjct: 184 ASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVY 243 Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302 R+LIFY+GAL VLL+LYPWD LL++L A GD YS SPFV+IFSLIGSD AA +LNFVVLT Sbjct: 244 RILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLT 303 Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362 AALSVYNSGVYCNSRMLYGLAEQGDAP++LMK+N +GVP+LA+G+SAL+TLLCV VNYL Sbjct: 304 AALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLF 363 Query: 363 PHEALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMV 422 P ALELL +L VAAL+INWA+ISL HL+FR+AM +QGV PSFKAFW PLSNYLCLAF+ Sbjct: 364 PQGALELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLAFVA 423 Query: 423 MIVGVMWMIPGIRASVYAIPVWVLVIWGFYLL 454 I+ +M +PGIR SV+AIPVWV +W Y L Sbjct: 424 GILIIMLWLPGIRMSVFAIPVWVGFLWLCYRL 455 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: 842 Number of extensions: 34 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: 464 Length adjustment: 33 Effective length of query: 433 Effective length of database: 431 Effective search space: 186623 Effective search space used: 186623 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