Align Serine transporter (characterized)
to candidate BWI76_RS22875 BWI76_RS22875 serine transporter
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__Koxy:BWI76_RS22875 Length = 429 Score = 787 bits (2033), Expect = 0.0 Identities = 400/429 (93%), Positives = 415/429 (96%) Query: 1 METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60 METTQTSTI S +RS WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA Sbjct: 1 METTQTSTIVSDATRSGWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60 Query: 61 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120 FPMTFFAHRG+TRFVLSGKNPGEDITEVVEEHFG+GAGKLITLLYFFAIYPILLVYSVAI Sbjct: 61 FPMTFFAHRGMTRFVLSGKNPGEDITEVVEEHFGVGAGKLITLLYFFAIYPILLVYSVAI 120 Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180 TNTVESFM HQL +TPPPRAILSLILIVGMMTIVRFGEQMIVKAMS+LVFPFV LM+LA Sbjct: 121 TNTVESFMLHQLHITPPPRAILSLILIVGMMTIVRFGEQMIVKAMSVLVFPFVVALMILA 180 Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240 YLIPQWNGAALETLSL +A+ATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG Sbjct: 181 FYLIPQWNGAALETLSLSSATATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240 Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300 AE+KCS ILA AHIMMVLTVMFFVFSCVLSL+PADLAAAK+QNISILSYLANHFNAPV Sbjct: 241 QGAEKKCSSILARAHIMMVLTVMFFVFSCVLSLSPADLAAAKDQNISILSYLANHFNAPV 300 Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360 IAWMAPIIA+IAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLN+ITALFMLVTT Sbjct: 301 IAWMAPIIAMIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNKITALFMLVTT 360 Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGH+SNVFVV+MGLIAI Sbjct: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHVSNVFVVIMGLIAI 420 Query: 421 SAIFYSLFS 429 SAIFYSLFS Sbjct: 421 SAIFYSLFS 429 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: 833 Number of extensions: 27 Number of successful extensions: 1 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: 429 Length adjustment: 32 Effective length of query: 397 Effective length of database: 397 Effective search space: 157609 Effective search space used: 157609 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