Align Serine transporter (characterized)
to candidate 200103 SO0919 serine transporter, putative (NCBI ptt file)
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__MR1:200103 Length = 430 Score = 469 bits (1208), Expect = e-137 Identities = 238/429 (55%), Positives = 308/429 (71%), Gaps = 7/429 (1%) Query: 1 METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60 +ET Q ST S R W + DT WML L+GTA+GAG+LFLPINAG+GG PL++MAI+ Sbjct: 9 LETPQ-STQESTTRRLPWTRQDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAIII 67 Query: 61 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120 PMT+ AHRGL+RFV S PG DIT+VVEEHFGIGAGK ITLLYF AIYPI+L+Y V I Sbjct: 68 GPMTYLAHRGLSRFVCSSSIPGSDITQVVEEHFGIGAGKAITLLYFLAIYPIVLIYGVGI 127 Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180 TNTV+SF+ +QLGM PPR +LS ILI GMM ++ GEQ ++K +LV+P VG+L ++ Sbjct: 128 TNTVDSFIVNQLGMASPPRFLLSGILIFGMMAVMVAGEQFMLKVTQLLVYPLVGILAFMS 187 Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240 +YLIP+W AL+ + +T + G T+WL IPV+VF+FNHSP IS F+V+ + ++G Sbjct: 188 VYLIPEWKMDALQVVP-ETGAFLG-----TVWLTIPVLVFAFNHSPAISQFSVSLKRDHG 241 Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300 A +K IL +M+V VM FVFSCVLSL+P LA AK +N+ ILSYLAN ++ Sbjct: 242 ANAARKADVILRNTSMMLVGFVMLFVFSCVLSLSPEQLAEAKAKNLPILSYLANVHDSGF 301 Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360 +++ P IA IAI SF GHY+GA EG G+++K LR K + +KLN+ +FM T Sbjct: 302 VSYFGPFIAFIAIVSSFFGHYMGATEGMKGIIVKQLRSSKKQVSEDKLNKFILVFMFATI 361 Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420 W VA NPSILGMIE LGGP+IA IL+LMPMYA+ KVPA++ Y ISNVFVV+ GL+A+ Sbjct: 362 WGVAIKNPSILGMIEALGGPVIAAILYLMPMYAVYKVPALKAYRHRISNVFVVIAGLLAM 421 Query: 421 SAIFYSLFS 429 +AI + L S Sbjct: 422 TAILFGLLS 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: 576 Number of extensions: 25 Number of successful extensions: 2 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: 430 Length adjustment: 32 Effective length of query: 397 Effective length of database: 398 Effective search space: 158006 Effective search space used: 158006 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