Align Serine transporter (characterized)
to candidate GFF1000 PS417_05070 serine/threonine protein kinase
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__WCS417:GFF1000 Length = 428 Score = 581 bits (1497), Expect = e-170 Identities = 297/417 (71%), Positives = 349/417 (83%), Gaps = 15/417 (3%) Query: 16 SAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFV 75 + W + DT WMLGLYGTAIGAG LFLPINAGVGG PLI++A+LAFPMTFFAHRGLTRFV Sbjct: 20 TGWTQYDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLIVLALLAFPMTFFAHRGLTRFV 79 Query: 76 LSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMT 135 LSGK+ DITEVVEEHFG+GAGKLITLLYFFAI+PILLVYSVA+TNT+ SFM HQL MT Sbjct: 80 LSGKSG--DITEVVEEHFGVGAGKLITLLYFFAIFPILLVYSVALTNTLGSFMEHQLHMT 137 Query: 136 PPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETL 195 PPPRAILSL+LI+G+M IVR G+ +IVKAMS+LV+PFV L+LLA LIP WNGA Sbjct: 138 PPPRAILSLVLILGLMAIVRCGQGVIVKAMSVLVYPFVASLLLLAFSLIPNWNGAFF--- 194 Query: 196 SLDTASATGNGLWM-----TLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKI 250 ++ G+G+ M TLWLAIPVMVFSFNHSPIIS+FAV ++ YG AE+K S I Sbjct: 195 -----ASAGDGMPMPLFFKTLWLAIPVMVFSFNHSPIISAFAVDQKRVYGAQAERKSSGI 249 Query: 251 LAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAI 310 LA AH MMVLTVMFF FSCVL+L+PADLAAAK QNISILSYLANHF PVIA+ AP+IA+ Sbjct: 250 LATAHGMMVLTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTPVIAYAAPLIAL 309 Query: 311 IAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSI 370 +AITKSFLGHY+GA EGF G+++KSLRG+ +S+ L R TALFM++T W VAT NPSI Sbjct: 310 VAITKSFLGHYIGASEGFQGLIVKSLRGRNRSMSAKWLERCTALFMVLTCWAVATFNPSI 369 Query: 371 LGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 L MIET+GGPIIA +LFLMPMYAI++VP++RKYSG +SNVFVVV+GLIA+SAI +S+ Sbjct: 370 LRMIETMGGPIIACLLFLMPMYAIRRVPSLRKYSGQVSNVFVVVIGLIALSAIVFSV 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: 668 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: 428 Length adjustment: 32 Effective length of query: 397 Effective length of database: 396 Effective search space: 157212 Effective search space used: 157212 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