Align Acetate uptake permease, ActP1; also takes up tellurite (characterized)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease
Query= TCDB::D5AU53 (551 letters) >FitnessBrowser__azobra:AZOBR_RS19235 Length = 556 Score = 788 bits (2035), Expect = 0.0 Identities = 404/553 (73%), Positives = 464/553 (83%), Gaps = 8/553 (1%) Query: 5 LLAAALAAM-----AGPALAAGEAIQGAVQQAPTNWTAIAMFLFFVVATLILTGWAARRT 59 LLAAA AA+ AGP AA AI GAV++ P N TAIAMFL FV TL +T WA++RT Sbjct: 6 LLAAASAALLPVLVAGPVHAA--AIDGAVERQPVNVTAIAMFLLFVAGTLGITYWASKRT 63 Query: 60 KSTADFYTAGGGITGFQNGLAIAGDYMSAAAFLGISGMVFAKGVDGAIYTVGFTVGWPFI 119 +S +DFYTAGGGI+GFQNGLAIAGDYMSAAAFLG+SGMVFAKG DG IYT+GF VGWP + Sbjct: 64 RSASDFYTAGGGISGFQNGLAIAGDYMSAAAFLGLSGMVFAKGFDGVIYTIGFLVGWPLM 123 Query: 120 LFLIAERLRNLGKFTFADITSFRLEQTRIRTLSALGALTVVVFYLIAQMVGAGKLIQLLF 179 LFLIAERLRNLG+FTFAD+ S+RL QT IR+L+A+G+LTVV FYLIAQMVGAGKLIQLLF Sbjct: 124 LFLIAERLRNLGRFTFADVASYRLGQTPIRSLAAVGSLTVVCFYLIAQMVGAGKLIQLLF 183 Query: 180 GLPYSYAVILVGVLMVLYVTFGGMLATTWVQIVKAVMLLSGATLLVILGLAQFGFSPERL 239 GL Y+YAV++VGVLM+LYVTFGGMLATTWVQI+KAVMLL G T+LV L LAQFGF+PERL Sbjct: 184 GLDYTYAVVMVGVLMILYVTFGGMLATTWVQIIKAVMLLGGCTVLVGLALAQFGFNPERL 243 Query: 240 MADALANHAKGAAILEPTPLVTDWVSGVSLALALMFGPAGLPHILMRFFTVPDAKEARKS 299 + A+A HA AAIL P+ + D ++ VSL+LALM GPAGLPHILMRFFTVPDAKEARKS Sbjct: 244 LQQAVAAHAANAAILRPSAAMADPIAAVSLSLALMCGPAGLPHILMRFFTVPDAKEARKS 303 Query: 300 VFYATGFVAYFFVLTTTIGFLAITLVGKNPEFLDAKG-IIGGGNMAAIHLAQAVGGNIFL 358 V YATGF+ YFF+LT TIGFLAI +VG NP +LDA G I+GGGNMAAIHL++A+GGN+FL Sbjct: 304 VVYATGFIGYFFILTVTIGFLAIVIVGTNPAYLDAAGKILGGGNMAAIHLSKAIGGNLFL 363 Query: 359 GFISAVAFATILAVVSGLALSGASAVAHDLYANVVKKGAAADKAEMRVSRIATLVLGVLA 418 GFISAVAFATILAVV+GL L+GASAV+HDLYA V+KKG A + +EMRVSR+ATL LGV+A Sbjct: 364 GFISAVAFATILAVVAGLTLAGASAVSHDLYARVLKKGNATEASEMRVSRLATLALGVIA 423 Query: 419 IVLGLMFENQNIAFMVGLAFGLAASVNFPVLLLSIFWKGMTTRGAFIGGLIGLVVSIVLV 478 I LGL+FENQNIAFMVGLAFGLAASVNFPVL+LSIFWKG+TTRGAFIGG GLV + V Sbjct: 424 ITLGLLFENQNIAFMVGLAFGLAASVNFPVLILSIFWKGLTTRGAFIGGFAGLVSCVAFV 483 Query: 479 VLGPAVWVDVFKFDTPIFPWSQYTLFSMATTFIAIWAFSVTDTSARAARDKAGYDAQFVR 538 VLGP VWV VFKF PIFP+ LFSM F W FSVTD SARAA + Y+ Q++R Sbjct: 484 VLGPTVWVSVFKFPAPIFPYEHPALFSMVIAFATTWLFSVTDRSARAAAEAKAYEYQYIR 543 Query: 539 SETGLGAAGAVAH 551 SETGLGAA A +H Sbjct: 544 SETGLGAASAASH 556 Lambda K H 0.328 0.140 0.414 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: 979 Number of extensions: 47 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: 551 Length of database: 556 Length adjustment: 36 Effective length of query: 515 Effective length of database: 520 Effective search space: 267800 Effective search space used: 267800 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: 53 (25.0 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