Align Serine transporter (characterized)
to candidate Pf1N1B4_1014 Serine transporter
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1014 Length = 433 Score = 583 bits (1503), Expect = e-171 Identities = 294/413 (71%), Positives = 346/413 (83%), Gaps = 5/413 (1%) Query: 14 SRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTR 73 + W K DT WMLGLYGTAIGAG LFLPINAGVGG PL+++A+LAFPMTFFAHRGLTR Sbjct: 23 THKGWSKHDTTWMLGLYGTAIGAGTLFLPINAGVGGFWPLLLLAVLAFPMTFFAHRGLTR 82 Query: 74 FVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLG 133 FVLSG++ DITEVVEEHFGIGAGKLITLLYFFAI+PILLVYSVA+TNT+ S M HQL Sbjct: 83 FVLSGRSG--DITEVVEEHFGIGAGKLITLLYFFAIFPILLVYSVALTNTLSSLMEHQLH 140 Query: 134 MTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALE 193 MTPPPRAILSL LI+G+M IVR G+ +IVK MS+LV+PFV L+LL + LIP WNGA Sbjct: 141 MTPPPRAILSLGLILGLMAIVRCGQGVIVKCMSVLVYPFVAALLLLGVSLIPNWNGAFFA 200 Query: 194 TLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAF 253 T S + TLWLAIPVMVFSFNHSPIIS+FAV +++ YG+ AE+K S ILA Sbjct: 201 TASEGMPLPL---FFKTLWLAIPVMVFSFNHSPIISAFAVDQKQRYGEQAERKSSGILAI 257 Query: 254 AHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAIIAI 313 AH+MMV+TVMFF FSCVL+L+PADLAAAK QNISILSYLANHF PVIA+ AP+IA++AI Sbjct: 258 AHLMMVVTVMFFCFSCVLALSPADLAAAKAQNISILSYLANHFQTPVIAYAAPLIALVAI 317 Query: 314 TKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSILGM 373 TKSFLGHY+GA EGF G+++KSLRG+G+ + + LNRITALFM+++ W VAT NPSILGM Sbjct: 318 TKSFLGHYIGASEGFQGLIVKSLRGRGRVMSASWLNRITALFMILSCWAVATFNPSILGM 377 Query: 374 IETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYS 426 IETLGGPIIA +LFLMPMYAI++VPA+R+YS SNVFVV++GLIA+SAI YS Sbjct: 378 IETLGGPIIACLLFLMPMYAIRRVPALRQYSNQASNVFVVLIGLIALSAIIYS 430 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: 679 Number of extensions: 24 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