Align Phenylacetate permease, Ppa (characterized)
to candidate WP_011385006.1 AMB_RS13215 cation acetate symporter
Query= TCDB::O50471 (520 letters) >NCBI__GCF_000009985.1:WP_011385006.1 Length = 554 Score = 639 bits (1647), Expect = 0.0 Identities = 318/523 (60%), Positives = 409/523 (78%), Gaps = 3/523 (0%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 +N TAI+MF FV TL +T WA+ RT+SASDFYTAGGG+TG QNGLAIAGD +SAA+ L Sbjct: 32 INVTAIAMFFAFVMGTLGITYWASKRTKSASDFYTAGGGITGFQNGLAIAGDYMSAATLL 91 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 G+S+M+F G+DG +Y + GWPIILFL+AERLRNLG+YTFAD+ SYRL Q+ VR + Sbjct: 92 GLSSMVFATGFDGFIYTISFFVGWPIILFLLAERLRNLGRYTFADIASYRLDQSKVRTFA 151 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 A G+L V YL+ QMVGAG+LI+LLFG+ Y AV++VGVLMV YVTFGGM+ATTWVQII Sbjct: 152 AMGSLTVVCFYLIVQMVGAGQLIKLLFGLDYAVAVIIVGVLMVVYVTFGGMIATTWVQII 211 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KA +LL G + + L FGFS E + A AV H G IM PG +L++PV A+SL LG Sbjct: 212 KACLLLGGGVLLCALALSKFGFSLENVAAKAVESHKAGVKIMGPGTMLADPVSAVSLSLG 271 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300 ++FGTA LPHILMRFFTV +AKEARKSVF A+GFIG+F+L++ ++G A+ +VGT+P + Sbjct: 272 LVFGTAALPHILMRFFTVPNAKEARKSVFVASGFIGFFFLIVCILGLAAVSIVGTDPQFF 331 Query: 301 D---ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDL 357 + G ++GGGNM +HLA+A+GG++FLGF+SAVAFATILAVV+GLAL+GASA++HD+ Sbjct: 332 EGGKVGGKLLGGGNMPVMHLAKALGGDIFLGFLSAVAFATILAVVSGLALAGASAIAHDI 391 Query: 358 YACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPV 417 YA VIR+G ATE EEMRVS++++L++G++AV+LG+MFE QN+AFL GL +AAS NFPV Sbjct: 392 YARVIRKGHATEAEEMRVSKLSSLVLGVVAVILGIMFEKQNVAFLVGLTFGIAASANFPV 451 Query: 418 LLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSL 477 L LSM+W+GLTT+GA+ G +AGL SAV VVL AVWV VL++ +FPY +PALFSM+L Sbjct: 452 LFLSMYWRGLTTKGALWGGIAGLVSAVTCVVLSKAVWVVVLNNPAPIFPYEHPALFSMTL 511 Query: 478 AFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 AFL V S D SE A E+ + Q++R+ TGIGAA AS H Sbjct: 512 AFLVTIVVSKLDGSETAKAEKALFDDQYVRAQTGIGAASASNH 554 Lambda K H 0.328 0.139 0.407 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: 888 Number of extensions: 46 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: 520 Length of database: 554 Length adjustment: 35 Effective length of query: 485 Effective length of database: 519 Effective search space: 251715 Effective search space used: 251715 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