Align Serine permease SerP1 (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP
Query= SwissProt::A2RI87 (459 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Length = 473 Score = 277 bits (709), Expect = 5e-79 Identities = 150/406 (36%), Positives = 237/406 (58%), Gaps = 26/406 (6%) Query: 5 QKNH--EAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFL 62 Q +H E +RGL+NRHIQLIA+ G IGTGLFLG+ ++ GPS+I Y + G F + Sbjct: 4 QNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIM 63 Query: 63 RTIGEMLYNDPSQHSFLNFVTKYSGIRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLP 122 R +GEM+ +P SF +F KY G G+ + W+ W++ + V +SELTA+G YI +W P Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP 123 Query: 123 HLPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAILGMIVTAIILVASNFHYTT 182 +P W+ L+ +N N + FGE EFWFA+IKV AI+GMI L+ S Sbjct: 124 DIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSG----- 178 Query: 183 VLSGKTVNDTASLNNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKS 242 AS+ N+++ FP+G V A+ ++MF+F +E +G TAAE PK Sbjct: 179 -----DGGPQASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTV 233 Query: 243 LPKAINQIPVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVIVFQLIGIKWA 293 +PKAINQ+ RIL+FY+GAL+ ++++ W + SPFV VF ++G A Sbjct: 234 IPKAINQVIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTA 293 Query: 294 AALINFVVLTSAASALNSSLFSATRNMYSLAKQHDKGRLTAFTKLSKAGIPINALYMATA 353 A ++NFVVLT+A S NS + +R + +A+Q D + A +K+ K G+P+ ++ + A Sbjct: 294 AHILNFVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPK--ALSKIDKRGVPVRSILASAA 351 Query: 354 LSLLAPVLT-LIPQIKNAFNFAASCTTNLFLVVYFITLYTYWQYRK 398 ++L+A +L L+PQ +A S ++ + + ++++++R+ Sbjct: 352 VTLVAVLLNYLVPQ--HALELLMSLVVATLVINWAMISFSHFKFRQ 395 Lambda K H 0.329 0.141 0.435 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: 555 Number of extensions: 34 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: 459 Length of database: 473 Length adjustment: 33 Effective length of query: 426 Effective length of database: 440 Effective search space: 187440 Effective search space used: 187440 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 (21.8 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