Align Serine transporter (characterized)
to candidate Pf1N1B4_4562 Serine transporter
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4562 Length = 426 Score = 549 bits (1415), Expect = e-161 Identities = 277/418 (66%), Positives = 339/418 (81%), Gaps = 8/418 (1%) Query: 10 ASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHR 69 A+ S +W + DT WMLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAFPMTF+AHR Sbjct: 15 ATPASLESWNRHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILAVLAFPMTFYAHR 74 Query: 70 GLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMS 129 GLTRFVLSG+ G DITEVVEEHFGI AG LITLLYFFAI+PILL+YSVA+TNTV SF+ Sbjct: 75 GLTRFVLSGRE-GADITEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLE 133 Query: 130 HQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNG 189 HQL + PPPRA+LS +LI+G++ +VR GEQ+IVKAMS++V+PF+ L+ LA++L+P WNG Sbjct: 134 HQLHIMPPPRAVLSFVLILGLLAVVRCGEQVIVKAMSLMVYPFIVALLFLAVFLVPHWNG 193 Query: 190 AALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSK 249 L T S S+ L TLWLAIPVMVFSFNHSPIIS+FAV ++ YG AE++ S+ Sbjct: 194 GILSTASTLPESSA---LLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGAHAEERSSQ 250 Query: 250 ILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIA 309 IL+ AH++MV+ V+FFVFSCVL+L+PA LA AK QN+SILSYLANHF+ P IA+ AP+IA Sbjct: 251 ILSRAHLLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNPTIAFAAPLIA 310 Query: 310 IIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPS 369 +AI+KSFLGHY+GA EG G++IKS GK L+R+TA FMLV WIVATLNPS Sbjct: 311 FVAISKSFLGHYIGASEGLKGLIIKS----GKRPAPKTLDRMTAAFMLVVCWIVATLNPS 366 Query: 370 ILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 ILGMIETLGGPIIA ILFLMPMYA++KVPAM ++ G SNVFV +GL+AISA+ YSL Sbjct: 367 ILGMIETLGGPIIAAILFLMPMYAVRKVPAMARFRGQASNVFVTAVGLVAISALIYSL 424 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: 638 Number of extensions: 33 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