Align Serine transporter (characterized)
to candidate PfGW456L13_3379 Serine transporter
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3379 Length = 396 Score = 545 bits (1404), Expect = e-160 Identities = 276/402 (68%), Positives = 333/402 (82%), Gaps = 8/402 (1%) Query: 26 MLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFVLSGKNPGEDI 85 MLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAFPMTF+AHRGLTRFVLSG+ G DI Sbjct: 1 MLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAFPMTFYAHRGLTRFVLSGRE-GADI 59 Query: 86 TEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMTPPPRAILSLI 145 TEVVEEHFGI AG LITLLYFFAI+PILL+YSVA+TNTV SF+ HQL +TPPPRA+LSL+ Sbjct: 60 TEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLEHQLHITPPPRAVLSLV 119 Query: 146 LIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETLSLDTASATGN 205 LI+G++ +VR GEQMIVKAMS++V+PF+ L+ LA+YLIP WNG L T S A + Sbjct: 120 LILGLLAVVRCGEQMIVKAMSLMVYPFIVALLFLAVYLIPHWNGGILATASQVPAPSA-- 177 Query: 206 GLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAHIMMVLTVMFF 265 L TLWLAIPVMVFSFNHSPIIS+FAV ++ YG+ AE++ S+IL+ AH++MV+ V+FF Sbjct: 178 -LLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGEHAEERSSQILSRAHLLMVVMVLFF 236 Query: 266 VFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAIIAITKSFLGHYLGAR 325 VFSCVL+L+PA LA AK QN+SILSYLANHF+ P IA+ AP+IA +AI+KSFLGHY+GA Sbjct: 237 VFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNPTIAFAAPLIAFVAISKSFLGHYIGAS 296 Query: 326 EGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSILGMIETLGGPIIAMI 385 EG G+++KS GK L+R+TA FMLV WIVATLNPSILGMIETLGGP+IA I Sbjct: 297 EGLKGLIVKS----GKRPSAKALDRMTAAFMLVVCWIVATLNPSILGMIETLGGPVIAAI 352 Query: 386 LFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 LFLMPMYAI+KVPAM +Y G SNVFV +GL+AISA+ YSL Sbjct: 353 LFLMPMYAIRKVPAMARYRGQASNVFVTAVGLVAISALVYSL 394 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: 597 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: 396 Length adjustment: 31 Effective length of query: 398 Effective length of database: 365 Effective search space: 145270 Effective search space used: 145270 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: 50 (23.9 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