Align Serine transporter (characterized)
to candidate AO353_15495 AO353_15495 serine/threonine protein kinase
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15495 Length = 433 Score = 577 bits (1488), Expect = e-169 Identities = 289/410 (70%), Positives = 344/410 (83%), Gaps = 5/410 (1%) Query: 18 WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFVLS 77 W K DT WMLGLYGTAIGAG LFLPINAGVGG PL+++A+LAFPMTFFAHRGLTRFVLS Sbjct: 27 WSKHDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLLVLALLAFPMTFFAHRGLTRFVLS 86 Query: 78 GKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMTPP 137 G++ DITEVVEEHFGIGAGKLITLLYFFAI+PILLVYSVA+TNT+ SFM HQL + PP Sbjct: 87 GRSG--DITEVVEEHFGIGAGKLITLLYFFAIFPILLVYSVALTNTLSSFMEHQLHIAPP 144 Query: 138 PRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETLSL 197 PR++LSL LI+G+M IVR G+ +IVK MS+LV+PFV L+LL + LIP WNGA + S Sbjct: 145 PRSVLSLALILGLMAIVRCGQGVIVKCMSVLVYPFVAALLLLGVSLIPNWNGAFFASASE 204 Query: 198 DTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAHIM 257 + TLWLAIPVMVFSFNHSPIIS+FAV +++ YG AE K S ILA AH M Sbjct: 205 GMPLPL---FFKTLWLAIPVMVFSFNHSPIISAFAVDQKQRYGTQAEPKSSGILAVAHSM 261 Query: 258 MVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAIIAITKSF 317 MVLTVMFF FSCVL+L+PADLAAAK QNISILSYLANHF PVIA+ AP+IA++AITKSF Sbjct: 262 MVLTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTPVIAYAAPLIALVAITKSF 321 Query: 318 LGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSILGMIETL 377 LGHY+GA EGF G+++KSLRG+G+ + + LNR+TALFM+++ W VAT NPSILGMIETL Sbjct: 322 LGHYIGASEGFQGLIVKSLRGRGRVMPTSWLNRVTALFMILSCWAVATFNPSILGMIETL 381 Query: 378 GGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 GGP+IA +LFLMPMYAI++VP++R+YSG SNVFVV++GLIA+SAI YS+ Sbjct: 382 GGPVIACLLFLMPMYAIRRVPSLRQYSGQASNVFVVLIGLIALSAIIYSV 431 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: 670 Number of extensions: 25 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: 429 Length of database: 433 Length adjustment: 32 Effective length of query: 397 Effective length of database: 401 Effective search space: 159197 Effective search space used: 159197 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