Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate GFF2643 Psest_2695 Sugar phosphate permease
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__psRCH2:GFF2643 Length = 447 Score = 268 bits (685), Expect = 3e-76 Identities = 146/429 (34%), Positives = 235/429 (54%), Gaps = 6/429 (1%) Query: 19 LDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMS 78 +D +I++A + + WL+ +C L++ DG D G + P + ++WG+ + G + S Sbjct: 4 VDVHEVIDNARFNGFHWLVVCLCALLLIFDGYDLFIYGVVLPVIMKEWGLTPLEAGALGS 63 Query: 79 AALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGL 138 AL GM+ GALV G ADR GRK+ +++ ++F T+ +++ +FRFL G+G Sbjct: 64 YALFGMMFGALVFGTLADRIGRKMGIAICFVLFSSATVLNGFASTPTEFGVFRFLAGLGC 123 Query: 139 GAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGW 198 G MPN L +EY P ++RS LV MF GY+LG + + +++P FGW ++F Sbjct: 124 GGLMPNVVALMNEYAPKKLRSTLVAVMFSGYSLGGMLSAGLGIYMLPRFGWEAMFFAAA- 182 Query: 199 APLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGTK 258 PL+L+ ++I++LPES FL+ +G+ T++ R +L+++ P + G + V + G Sbjct: 183 VPLLLLPVIIWYLPESVGFLVRQGR-TEQARALLNKVDPTRQLGANDELVMSD--IKGKS 239 Query: 259 KGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQF 318 V + + V+ TV +WV +F L+M+Y L SWLP LM G SL + F Sbjct: 240 ASVLELFRDGRGVR-TVSIWVAFFCCLLMVYALGSWLPKLMANAGYSLGSSLSFLLALNF 298 Query: 319 GGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGIAVNGA 378 GG+ A+ GW DRFN ++++ F+ + + ++G P L L I AG V G Sbjct: 299 GGMAGAILGGWLGDRFNLSKVVVVFFAISVVSISLLGFKTPMPVLYTL-IFIAGATVIGT 357 Query: 379 QSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLIIPA 438 Q + +A+FY R+TG+ W SGIGR GA+ G +G LLG N + +P Sbjct: 358 QILLYATAAQFYGLSIRSTGLGWASGIGRNGAIVGPLLGGALLGINLPLQLNFMAFAVPG 417 Query: 439 AAAAIAIFV 447 AA+A+ V Sbjct: 418 IIAALAMSV 426 Lambda K H 0.328 0.141 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: 659 Number of extensions: 39 Number of successful extensions: 8 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: 457 Length of database: 447 Length adjustment: 33 Effective length of query: 424 Effective length of database: 414 Effective search space: 175536 Effective search space used: 175536 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: 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