Align Histidine permease HisP (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= SwissProt::A2RI97 (477 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 323 bits (829), Expect = 6e-93 Identities = 175/457 (38%), Positives = 267/457 (58%), Gaps = 25/457 (5%) Query: 8 KRNLKQRHITMIALGGTIGTGLFLTSGATISQAGPWGAVLAYCFIGIMVYFVMTSLGEMA 67 K+ ++ RHI M+ALGG IGTGLFLTSG T++QAGP GAV+AY +MVY VM LGE+A Sbjct: 15 KQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLGELA 74 Query: 68 TYLPTSGSFSDYGGRYVDPAFGFALGWNYWLNGAITIAVDLTTAGLITQFWFPHLPSWIF 127 +P +GSFS Y R++ P G+ + W YWL + I + T AG++ WFP P WI+ Sbjct: 75 VQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPVWIW 134 Query: 128 SGIATVLIFIINVMAVGAFGETEYWLSTIKVITIVLFLAIGLLTIFGVLGQGNVDVVANL 187 S + ++F+ NV++V F ETE+WLS IKV+T+V+FL IG I G+L N+D ++ Sbjct: 135 SALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLL---NIDQAHSI 191 Query: 188 TAGNHG----FVGGISGFVGVLLIAGFSFQGTEMLGITAGESEDPGKTIPKAMNSIFWRI 243 N F G LL F+F GTE++GI AGE++DP + +P+A+ + R+ Sbjct: 192 GLSNFTREGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRL 251 Query: 244 LLFYIFSIIVIAAIINFKDPRLLNPSSTAVMSPFTIVFKNIGFAVAASVMNAVILTSVIS 303 +F++ +I V+A ++ PR + V SPF VF IG +A +MN VI+++++S Sbjct: 252 AVFFVGTIFVLATLL----PR---EQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLS 304 Query: 304 SANSVMYASTRILYSLGQEKGAPKFFGRTAKNGIPFYALLATTIICFIAFLTGIFGTQ-I 362 +ANS +YA++R+L++L + PK F + G P A++ + + L+ +F I Sbjct: 305 AANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTI 364 Query: 363 YLFLIDLSSLTGFLAWLGISVSHIRFRRAYIAQGKKLEDLPYKAKWFPFGPIVALL--MT 420 YL L+ +S L + W+ I+ S I FRR Y+A G + L ++ + +P+ P+ AL+ Sbjct: 365 YLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSL 424 Query: 421 GAIAINLDPAMLFSEHWGEGLALYAAIPIFIVLYFGY 457 I I DP + +ALY +P YF Y Sbjct: 425 ACIGIAFDPE--------QRVALYFGLPFIAWCYFVY 453 Lambda K H 0.327 0.142 0.438 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: 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: 477 Length of database: 476 Length adjustment: 33 Effective length of query: 444 Effective length of database: 443 Effective search space: 196692 Effective search space used: 196692 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 (21.7 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