Align Phenylacetate permease, Ppa (characterized)
to candidate WP_011385106.1 AMB_RS13720 cation acetate symporter
Query= TCDB::O50471 (520 letters) >NCBI__GCF_000009985.1:WP_011385106.1 Length = 561 Score = 678 bits (1750), Expect = 0.0 Identities = 340/522 (65%), Positives = 419/522 (80%), Gaps = 3/522 (0%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 NW AI MF++FV TL +T WAA RT++A+DFY AGGG+TG QNGLAIAGD +SAASFLG Sbjct: 40 NWHAIIMFVIFVGMTLGITYWAAGRTKTAADFYAAGGGITGFQNGLAIAGDYMSAASFLG 99 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 ISA+++ +GYDGL++++G L GWPIILFLIAERLRNLGKYTFADV YRLA+TP+R +A Sbjct: 100 ISALVYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKYTFADVCGYRLARTPIRTFAA 159 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 G+L+V + YL+ QMVGAG+LI+LLFG+ Y+YAVM+VG LM+ YVTFGGM+ATTWVQIIK Sbjct: 160 TGSLIVVIFYLIGQMVGAGQLIKLLFGMDYIYAVMIVGALMMVYVTFGGMVATTWVQIIK 219 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 A +LL G +F+AF V+ HFGFS E +F A+ VH K AIMAPG L++NPVDAISLG+ + Sbjct: 220 ACLLLGGATFIAFGVMSHFGFSFEKLFVKAIEVHPKKVAIMAPGALVTNPVDAISLGMAL 279 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSY-R 300 MFGTAGLPHILMRFFTV DA+EARKSVFYATGFIGYFY+L +IGFGAI +V T P Y Sbjct: 280 MFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYILTFIIGFGAITLVATNPEYLT 339 Query: 301 DATGA--IIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLY 358 G+ + GG NM AV LA A+GG+LFLGFISAVAFATILAVV+GL L+GASA+SHDLY Sbjct: 340 KGLGSLDLKGGNNMAAVWLAHAIGGDLFLGFISAVAFATILAVVSGLTLAGASAISHDLY 399 Query: 359 ACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVL 418 A VI G+ATE E+ VS+IA++ +G++AVLLGL+FE QN+AF+ L +VAAS NFPVL Sbjct: 400 ASVIMHGQATEGREVTVSKIASIGLGIIAVLLGLVFEKQNVAFIVALTFSVAASANFPVL 459 Query: 419 LLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLA 478 +LSMFW GLTTRGAV G M GL +V++VVL AVWV + +FP++ PALFS+ A Sbjct: 460 VLSMFWGGLTTRGAVLGGMIGLLMSVIMVVLSKAVWVQSFGFKAEIFPFAYPALFSVPAA 519 Query: 479 FLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 F +W+FS+ D+S +A ER Y AQ IRS TG+GA GA+ H Sbjct: 520 FFFSWLFSILDNSPQAQAERAAYEAQSIRSETGLGAEGAASH 561 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: 951 Number of extensions: 41 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: 561 Length adjustment: 35 Effective length of query: 485 Effective length of database: 526 Effective search space: 255110 Effective search space used: 255110 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