Align Serine transporter (characterized)
to candidate 5208227 Shew_0739 aromatic amino acid permease (RefSeq)
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__PV4:5208227 Length = 423 Score = 466 bits (1199), Expect = e-136 Identities = 232/429 (54%), Positives = 308/429 (71%), Gaps = 6/429 (1%) Query: 1 METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60 M+ T + + R W ++DT WML L+GTA+GAG+LFLPINAG+GG PL++MA++ Sbjct: 1 MQNEATISDVNLAQRQGWTRSDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAVII 60 Query: 61 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120 PMT+ AHRGL+RFV S + G DIT VVEE+FG+GAGK ITLLYFFAIYPI+L+Y V I Sbjct: 61 GPMTYLAHRGLSRFVCSSQRQGSDITHVVEEYFGVGAGKAITLLYFFAIYPIVLIYGVGI 120 Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180 TNTV+SF+ +QLGM PPR +LS IL++GMM+++ GE+ ++K +LV+P VG+L ++ Sbjct: 121 TNTVDSFIVNQLGMASPPRFLLSGILVLGMMSVMVSGEKFMLKVTQLLVYPLVGILAFMS 180 Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240 LYLIP W AL + A G L T+WL IPV+VF+FNHSP IS F+V+ +++YG Sbjct: 181 LYLIPSWKMDALMEVP-----AAGEFLG-TVWLTIPVLVFAFNHSPAISQFSVSLKKQYG 234 Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300 A +K IL +M+V VM FVFSCVLSL+PA LA AK QN+ ILSYLAN + Sbjct: 235 SNAAKKADVILRNTSMMLVGFVMLFVFSCVLSLSPAQLAEAKAQNLPILSYLANVHASGF 294 Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360 +++ PIIA+IAI SF GHYLGA EG G++ K LR K + K+++ FM +T Sbjct: 295 VSYFGPIIAVIAIVSSFFGHYLGATEGLKGIITKQLRSSNKEVSDAKIDKFILGFMFLTI 354 Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420 W VA +NPSILGMIE LGGPIIA IL+LMPMYA+ KVPA++ Y G ISN+ V++ GL+A+ Sbjct: 355 WGVAVINPSILGMIEALGGPIIAAILYLMPMYAVYKVPALKAYRGRISNILVILAGLLAM 414 Query: 421 SAIFYSLFS 429 +AI + + S Sbjct: 415 TAILFGMLS 423 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: 587 Number of extensions: 27 Number of successful extensions: 3 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: 423 Length adjustment: 32 Effective length of query: 397 Effective length of database: 391 Effective search space: 155227 Effective search space used: 155227 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