Align PTS lactose transporter subunit IIC, component of PTS-type lactose transporter, IIC-IIB-IIA (characterized)
to candidate 5208407 Shew_0919 diguanylate phosphodiesterase (RefSeq)
Query= TCDB::U5MFA1 (445 letters) >FitnessBrowser__PV4:5208407 Length = 707 Score = 129 bits (323), Expect = 4e-34 Identities = 107/417 (25%), Positives = 192/417 (46%), Gaps = 59/417 (14%) Query: 19 NSYRYIMAIKSAFITLMPVIIVGAFSVLISNMV--LDPK-NGLASFSSLS----FLAALK 71 +S +++AIK +FI L+P I V + LI +V P G A+++ LS L + Sbjct: 7 SSSLFLIAIKESFIALLPFIFVNSLLALIVALVDVWQPSWQGSAAYAWLSQFGRLLFSFF 66 Query: 72 PITS--ALNYATLNFLNIGAVFLIGIELGRINGIKSLFPGLLAVICFICVTPTTVEMMVD 129 P+ + +L++ +L++ AV + + +G + + + + Sbjct: 67 PLMALLSLSFHFAKYLHVSAVVVASLSIG-----------------------SQIALHIH 103 Query: 130 GQMHV-VKDVLLRQFSDTRSLFLGMFIAILSVEIYCWLEGRKGLKIKMPDTVPPNVSASF 188 G + + + F D R++ + +A L L K L + ++ + Sbjct: 104 GSEAIDLSNGFDFLFGDARAIITPILVAYLLQR----LMAIKALSLLQSTSLSSYLKLHL 159 Query: 189 SALIPAIITTTAIATFGFLFHQLTGMYLYDAVYQVVQQPLERVVQSLPGILLLMFVAQLF 248 + IP I+ + T + +L GM L V + +L + + + + Sbjct: 160 NLFIPLILCFVLVTTGIYWVGELLGMVLSPLVDSLAAS------STLLQLFVRVLATHVL 213 Query: 249 WVIGIHGNQMIKPIREPLLLGAITVNMSAFEQGKE--VPNIITMPFWDVYMSIGGSGLTI 306 W G+HG+ I L+LG + G + PN+ F D+++ +GGSG T Sbjct: 214 WCFGVHGD-----IAYMLVLGV--------DNGLQQVAPNLTLSQFTDLFVLLGGSGATH 260 Query: 307 GLLIAVMIATRRKEMKEIAKLSIGPGLFNINEPVIFGMPIMLNPILAIPFIITPLVTGSI 366 LLIA+ IA++ K +AKL++ LFNINE +I+G+PI+ NP L +PF++ PL I Sbjct: 261 SLLIALFIASKDKNAVNVAKLALPFALFNINEILIYGLPIIFNPRLMLPFVLVPLFNTLI 320 Query: 367 GYFATLTGFAGKAVVMVPWTTPPLINAWLSTAGSMGAVVTQLICIVVAVLIYLPFVK 423 G ++G+ A W TP +N +++ G++ + QL+ + V IYLPFV+ Sbjct: 321 GTLLIVSGWVSFAGNDFAWITPIFLNGYVA-GGTLALPLVQLLLVCAGVFIYLPFVR 376 Lambda K H 0.328 0.142 0.419 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: 598 Number of extensions: 34 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 707 Length adjustment: 36 Effective length of query: 409 Effective length of database: 671 Effective search space: 274439 Effective search space used: 274439 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: 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