Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= TCDB::M1IW84 (556 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 266 bits (680), Expect = 1e-75 Identities = 161/473 (34%), Positives = 253/473 (53%), Gaps = 22/473 (4%) Query: 12 DTQPHLRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIG-FFVFFVLR 70 +T+ ++++ RHI ++A+GG IGTGLF+ SG T++ AGP V+ IIG V+ V+ Sbjct: 9 NTRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMM 68 Query: 71 AMGELLLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPG 130 +GEL + SF +A LGP G+ V W YW W V ++ A W+P Sbjct: 69 CLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPD 128 Query: 131 LPIWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVC--LIAVGAILVATNFVSP 188 P+W+ + + ++ N+ SVR F E EFW +LIKV +V LI GAIL N Sbjct: 129 TPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQA 188 Query: 189 HGVHATIENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAIN 248 H + + N + G FPTGF+ + FA+ G EL+G AA ET DP+R +PRAI Sbjct: 189 HSIG--LSNFTRE-GLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIR 245 Query: 249 AVPLRVAVFYIGALLAILAVVPWRQFASGESPFVTMFSLAGLAAAASVVNFVVVTAAASS 308 LR+AVF++G + + ++P Q ESPFVT+F+ G+ +A ++NFV+++A S+ Sbjct: 246 TTVLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSA 305 Query: 309 ANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLT----APLLLTSIPLLYAGR 364 ANSG ++ RML+ L+D+GH P F L R G P A++++ A LL+S+ +A Sbjct: 306 ANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSV---FAAD 362 Query: 365 SVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTD---SVYKMPGGVVMCWAVL 421 ++ + + ++S L + VW I S + +RR + D +++ G + L Sbjct: 363 TI---YLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGAL 419 Query: 422 VFFAFVIWTLTTETETATALAWFPLWFVLLA--VGWLVTQRRQSRRSFGFHCQ 472 V + + + E AL +F L F+ V ++ + R+ R S F Q Sbjct: 420 VCCSLACIGIAFDPEQRVAL-YFGLPFIAWCYFVYYITRKSRERRLSVAFVAQ 471 Lambda K H 0.328 0.140 0.442 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: 634 Number of extensions: 28 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: 556 Length of database: 476 Length adjustment: 35 Effective length of query: 521 Effective length of database: 441 Effective search space: 229761 Effective search space used: 229761 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: 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