Align Serine transporter (characterized)
to candidate 6938669 Sama_2772 amino acid transporter, transmembrane (RefSeq)
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__SB2B:6938669 Length = 438 Score = 466 bits (1200), Expect = e-136 Identities = 230/418 (55%), Positives = 307/418 (73%), Gaps = 6/418 (1%) Query: 10 ASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHR 69 A+ ++ W DT WML L+GTA+GAG+LFLPINAG+GG PL++MA+L PMT+ AHR Sbjct: 25 ATPNNAMPWTAQDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVVMALLIGPMTYLAHR 84 Query: 70 GLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMS 129 GL+RFV S G DIT+VVEEHFG GAGK IT+LYFFAIYPI+L+Y V ITN V+SFM Sbjct: 85 GLSRFVCSSSIAGSDITQVVEEHFGKGAGKAITVLYFFAIYPIVLIYGVGITNVVDSFMV 144 Query: 130 HQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNG 189 +QLG+ PR +LS +LI+GMM+++ GE++++K LV+P V +L ++LYL+P WN Sbjct: 145 NQLGLESLPRWLLSGVLILGMMSVMVAGEKIMLKVTQFLVYPLVAILAFMSLYLMPNWNL 204 Query: 190 AALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSK 249 AA++ + A G+ L T+WL IPV++F+FNHSP IS FAV+ + ++G A +K Sbjct: 205 AAVKEVP-----AVGDFLG-TIWLTIPVLIFAFNHSPAISQFAVSLKRDHGSNASRKADI 258 Query: 250 ILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIA 309 IL +M+V VM FVFSCVLSL+PA LA AK QN+ ILSYLAN F++ +++ P IA Sbjct: 259 ILRNTAMMLVGFVMLFVFSCVLSLSPAQLAEAKSQNLPILSYLANVFDSGFVSYFGPFIA 318 Query: 310 IIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPS 369 +AI SF GHY+GA EG +G++ K L GKGK ++ KLNR FM +T W VA +NPS Sbjct: 319 FVAIVSSFFGHYMGASEGMSGIIKKQLEGKGKPVDEGKLNRFILGFMFLTIWAVAVINPS 378 Query: 370 ILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSL 427 ILGMIE LGGPIIA IL+LMPMYA+ +VPA++ Y G ISN+FV++ GL++++AI Y L Sbjct: 379 ILGMIEALGGPIIAAILYLMPMYAVYRVPALKAYRGRISNIFVIIAGLLSMTAILYGL 436 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: 619 Number of extensions: 23 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: 438 Length adjustment: 32 Effective length of query: 397 Effective length of database: 406 Effective search space: 161182 Effective search space used: 161182 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 Apr 09 2024. 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