Align S-adenosylmethionine permease SAM3 (characterized)
to candidate AO356_11625 AO356_11625 GABA permease
Query= CharProtDB::CH_091257 (587 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_11625 Length = 464 Score = 201 bits (510), Expect = 7e-56 Identities = 128/421 (30%), Positives = 212/421 (50%), Gaps = 17/421 (4%) Query: 77 LSQRHLTMIAIGGTLGTGLFIGLGYSLASGPAALLIGFLLVGTSMFCVVQSAAELSCQFP 136 L RH+TM++I G +G GLF+G G+++A+ A+L+ + G + V++ E++ P Sbjct: 14 LKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEMAVASP 73 Query: 137 VSGSYATHVSRFIDESVGFTVATNYALAWLISFPSELIGCALTISYWNQTVNPAVWVAIF 196 +GS++T+ R I GFT+ Y W++ P E A + W V V+ + Sbjct: 74 DTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWVFTLVI 133 Query: 197 YVFIMVLNLFGVRGFAETEFALSIIKVIAIFIFIIIGIVLIAGGGPNSTGYIGAKYWHDP 256 + + V NLF V+ + E EF +++KV+AI FI +G++ I G P S G + D Sbjct: 134 TLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGLMAIFGVLPTSQ-VSGVSHLFDT 192 Query: 257 GAFAKPVFKNLCNTFVSAAFSFGGSELVLLTSTESKNI-SAISRAAKGTFWRIAIFYITT 315 F + ++ FSF G+E+V + + ESKN IS+A WRI +FY+ + Sbjct: 193 QGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGLFYLVS 252 Query: 316 VVIIGCLVPYNDPRLLSGSNSEDVSASPFVIALSNTGSMGAKVSNFMNVVILVAVVSVCN 375 + I+ LVP+NDP L S + + V L G AK+ +++V+LVAV S N Sbjct: 253 IFIVVALVPWNDPLLASVGSYQTV--------LERMGIPNAKL--IVDIVVLVAVTSCLN 302 Query: 376 SCVYASSRLIQALGASGQLPSVCSYMDRKGRPLVGIGISGAFGLLGFLVASKKEDEVFTW 435 S +Y +SR++ +LG G P+V ++ G P + +S L VF + Sbjct: 303 SALYTASRMMFSLGKRGDAPAVSQRTNKSGTPHWAVMLSTGAAFLAVFANYVAPAAVFEF 362 Query: 436 LFALCSISSFFTWFCICMSQIRFRMALKAQGRSNDEIAYKSIL--GVYGGILGCVLNALL 493 L A + + I +SQ+R R A+G ++IA+ L G+ ++ ++ AL Sbjct: 363 LLASSGAIALLVYLVIAVSQLRMRKQRMARG---EKIAFSMWLFPGLTYAVIVFIVGALT 419 Query: 494 I 494 I Sbjct: 420 I 420 Lambda K H 0.324 0.138 0.417 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: 577 Number of extensions: 30 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: 587 Length of database: 464 Length adjustment: 35 Effective length of query: 552 Effective length of database: 429 Effective search space: 236808 Effective search space used: 236808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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