Align Serine transporter (characterized)
to candidate AO356_24385 AO356_24385 serine/threonine protein kinase
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24385 Length = 426 Score = 550 bits (1418), Expect = e-161 Identities = 279/428 (65%), Positives = 345/428 (80%), Gaps = 14/428 (3%) Query: 2 ETTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAF 61 ETT +T+ S W + DT WMLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAF Sbjct: 13 ETTVPATL------SQWSRQDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAF 66 Query: 62 PMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAIT 121 PMTF+AHRGLTRFVLSG++ G DITEVVEEHFG+ AG LITLLYFFAI+PILL+YSVA+T Sbjct: 67 PMTFYAHRGLTRFVLSGRD-GADITEVVEEHFGLKAGALITLLYFFAIFPILLIYSVALT 125 Query: 122 NTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLAL 181 NTV SF+ HQL + PPPRA+LSL+LI+G++ +VR GEQ IVKAMS++V+PF+ L+ LA+ Sbjct: 126 NTVGSFLEHQLHIQPPPRAVLSLVLILGLLAVVRCGEQAIVKAMSLMVYPFIVALLFLAV 185 Query: 182 YLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGD 241 +LIP W+G L T S + L TLWLAIPVMVFSFNHSPIIS+FAV ++ YG Sbjct: 186 FLIPHWSGGILSTASTPPEPSA---LLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGA 242 Query: 242 MAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVI 301 AE++ S+IL+ AH++MV+ V+FFVFSCVL+LTPA LA AK QN+SILSYLANHF+ P I Sbjct: 243 NAEERSSQILSRAHVLMVVMVLFFVFSCVLTLTPAQLAEAKAQNLSILSYLANHFSNPTI 302 Query: 302 AWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTW 361 A+ AP+IA +AI+KSFLGHY+GA EG G+++KS G+ L+R+TA FMLV W Sbjct: 303 AFAAPLIAFVAISKSFLGHYIGASEGLKGLIVKS----GRRPAPKTLDRLTAAFMLVVCW 358 Query: 362 IVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAIS 421 IVATLNPSILGMIETLGGP+IA ILFLMPMYAI+KVPAM +Y G SNVFVV++GL+AI+ Sbjct: 359 IVATLNPSILGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVVLVGLVAIT 418 Query: 422 AIFYSLFS 429 A+ YSL + Sbjct: 419 ALVYSLMA 426 Lambda K H 0.328 0.140 0.416 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: 628 Number of extensions: 30 Number of successful extensions: 4 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: 429 Length of database: 426 Length adjustment: 32 Effective length of query: 397 Effective length of database: 394 Effective search space: 156418 Effective search space used: 156418 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