Align PTS lactose transporter subunit IIC, component of PTS-type lactose transporter, IIC-IIB-IIA (characterized)
to candidate 15855 b1737 N,N'-diacetylchitobiose-specific enzyme IIC component of PTS (NCBI)
Query= TCDB::U5MFA1 (445 letters) >FitnessBrowser__Keio:15855 Length = 452 Score = 217 bits (553), Expect = 5e-61 Identities = 141/454 (31%), Positives = 237/454 (52%), Gaps = 44/454 (9%) Query: 14 FATTFNSYRYIMAIKSAFITLMPVIIVGAFSVLISNMVLDPKNGLASFS--------SLS 65 FA ++ AIK+ FI LMP+ + GA VLI+N+ L G +S ++ Sbjct: 15 FAVKIGKQPHVNAIKNGFIRLMPLTLAGAMFVLINNVFLSFGEGSFFYSLGIRLDASTIE 74 Query: 66 FLAALKPITSALNYATLNFLNIGAVFLIGIELGRINGIKSLFPGLLAVICFICVTPTTVE 125 L LK I + TL +++ A F IG+ L + +L GLL+V F+ VTP +V Sbjct: 75 TLNGLKGIGGNVYNGTLGIMSLMAPFFIGMALAEERKVDALAAGLLSVAAFMTVTPYSV- 133 Query: 126 MMVDGQMHVVKDVLLRQFSDTRSLFLGMFIAILSVEIYCWLEGRKGLKIKMPDTVPPNVS 185 G+ + V + ++ G+ I ++ E++ ++ R+ IK+PD+VP +VS Sbjct: 134 ----GEAYAVG----ANWLGGANIISGIIIGLVVAEMFTFIV-RRNWVIKLPDSVPASVS 184 Query: 186 ASFSALIPAIITTT-------AIATFGFLFHQLTGMYLYDAVYQVVQQPLERVVQSLPGI 238 SFSALIP I + A+ T+G FHQ+ + + PL + S+ G Sbjct: 185 RSFSALIPGFIILSVMGIIAWALNTWGTNFHQI--------IMDTISTPLASL-GSVVGW 235 Query: 239 LLLMFVAQLFWVIGIHGNQMIKPIREPLLLGAITVNMSAFEQGKEVP---------NIIT 289 ++FV L W GIHG + + ++ N++ ++Q V +I Sbjct: 236 AYVIFVP-LLWFFGIHGALALTALDNGIMTPWALENIATYQQYGSVEAALAAGKTFHIWA 294 Query: 290 MPFWDVYMSIGGSGLTIGLLIAVMIATRRKEMKEIAKLSIGPGLFNINEPVIFGMPIMLN 349 P D ++ +GGSG T+GL++A+ IA+RR + +++AKL++ G+F INEP++FG+PI++N Sbjct: 295 KPMLDSFIFLGGSGATLGLILAIFIASRRADYRQVAKLALPSGIFQINEPILFGLPIIMN 354 Query: 350 PILAIPFIITPLVTGSIGYFATLTGFAGKAVVMVPWTTPPLINAWLSTAGSMGAVVTQLI 409 P++ IPF++ + +I A G + PWT P + A+ +T GS+ A++ L Sbjct: 355 PVMFIPFVLVQPILAAITLAAYYMGIIPPVTNIAPWTMPTGLGAFFNTNGSVAALLVALF 414 Query: 410 CIVVAVLIYLPFVKIATRRADAAQRQVDNQQTAN 443 + +A LIYLPFV +A + +A ++ + AN Sbjct: 415 NLGIATLIYLPFVVVANKAQNAIDKEESEEDIAN 448 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: 507 Number of extensions: 26 Number of successful extensions: 5 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: 445 Length of database: 452 Length adjustment: 33 Effective length of query: 412 Effective length of database: 419 Effective search space: 172628 Effective search space used: 172628 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: 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