Align Serine transporter (characterized)
to candidate AO353_21595 AO353_21595 serine/threonine protein kinase
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21595 Length = 426 Score = 553 bits (1424), Expect = e-162 Identities = 283/419 (67%), Positives = 342/419 (81%), Gaps = 10/419 (2%) Query: 10 ASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHR 69 A+ S S+W + DT WMLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAFPMTF+AHR Sbjct: 15 AAPASLSSWNRHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILALLAFPMTFYAHR 74 Query: 70 GLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMS 129 GLTRFVLSG+ G DITEVVEEHFGI AG LITLLYFFAI+PILL+YSVA+TNTV SF+ Sbjct: 75 GLTRFVLSGR-AGADITEVVEEHFGIKAGALITLLYFFAIFPILLIYSVALTNTVGSFLE 133 Query: 130 HQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNG 189 HQL + PPPRAILS +LI+G++ +VR GEQMIVKAMS++V+PF+ L+ LA++LIP WNG Sbjct: 134 HQLHIMPPPRAILSFVLILGLLAVVRCGEQMIVKAMSLMVYPFIVALLFLAVFLIPHWNG 193 Query: 190 AALETLS-LDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCS 248 LET S L SA L TLWLAIPVMVFSFNHSPIIS+FAV ++ YG AE++ S Sbjct: 194 GILETASTLPEPSA----LLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGAHAEERSS 249 Query: 249 KILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPII 308 +IL+ AH +MV+ V+FFVFSCVL+L+PA LA AK QN+SILSYLANHF+ P IA+ AP+I Sbjct: 250 QILSRAHTLMVVMVLFFVFSCVLTLSPAQLAEAKAQNLSILSYLANHFSNPTIAFAAPLI 309 Query: 309 AIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNP 368 A +AI+KSFLGHY+GA EG G+++KS G+ L+R+TA FMLV WIVATLNP Sbjct: 310 AFVAISKSFLGHYIGASEGLKGLIVKS----GRRPAPKTLDRMTAAFMLVVCWIVATLNP 365 Query: 369 SILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 SILGMIETLGGP+IA ILFLMPMYAI+KVPAM +Y G SNVFV ++GL+AISA+ YSL Sbjct: 366 SILGMIETLGGPVIAAILFLMPMYAIRKVPAMARYRGQASNVFVTLVGLVAISALIYSL 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: 631 Number of extensions: 31 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