Align PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component (characterized)
to candidate BWI76_RS14945 BWI76_RS14945 PTS system, cellobiose-specific IIC component
Query= SwissProt::P17334 (452 letters) >FitnessBrowser__Koxy:BWI76_RS14945 Length = 439 Score = 226 bits (577), Expect = 9e-64 Identities = 143/446 (32%), Positives = 234/446 (52%), Gaps = 30/446 (6%) Query: 1 MSNVIASLEKVLLPFAVKIGKQPHVNAIKNGFIRLMPLTLAGAMFVLINNVFLSFGEGSF 60 M+NV+ LE L+P A K +Q H+ AI+ ++ MP + G++ ++I+ SF S+ Sbjct: 1 MNNVLGFLEAKLMPLAAKTAQQRHLGAIRGAYVSFMPFIIVGSILLVIS----SFPNQSY 56 Query: 61 FYSLGIRLDASTIETLNGLKGIGGNVYNGTLGIMSLMAPFFIGMALAEERKVDALAAGLL 120 + AS + +N MSL F + LAE D ++ G+L Sbjct: 57 QQFMASTFGASWSAIIE-------IPFNAVFSTMSLFISFLVAYRLAEHYGDDRISCGIL 109 Query: 121 SVAAFMTVTPY----SVGEAYAVGANWLGGANIISGIIIGLVVAEMFTFIVRRNWVIKLP 176 S+ F+ +TP+ G + W+G + +I L+ E+F ++ R+ VIK+P Sbjct: 110 SLVGFLILTPFIKVAENGGITVIPVEWIGTKGLFVAMIGSLLWTELFCWLKRKKLVIKMP 169 Query: 177 DSVPASVSRSFSALIPGFIILS-VMGIIAWALNTWGTNFHQIIMDTISTPLASLG-SVVG 234 D VP +V SF+ALIP +++ ++ I +T HQ I + +++P+ G S G Sbjct: 170 DGVPPAVQESFAALIPALLVMILILAIRIGFEHTHYATIHQFIYEVVASPVRHYGTSYFG 229 Query: 235 WAYVIF-VPLLWFFGIHGALALTALDNGIMTPWALENIATYQQYGSVEAALAAGKTFHIW 293 +F + +LW GI+ ++ NGI+ P +EN Q ++ A A HI Sbjct: 230 ALMTVFSITILWSVGINSG----SMINGIIRPLWMEN-----QTDNIAAIQAGVTPPHII 280 Query: 294 AKPMLDSFIFLGGSGATLGLILAIFIASRRADYRQVAKLALPSGIFQINEPILFGLPIIM 353 + D I++GG+GATL L++A+ I +R + R+VA+L + IF INEPILFGLP+IM Sbjct: 281 TEQFFD-MIWMGGAGATLSLVIAMLIFARSKNMREVARLGAGASIFNINEPILFGLPVIM 339 Query: 354 NPVMFIPFVLVQPILAAITLAAYYMGIIPPVTNI-APWTMPTGLGAFFNTNGSVAALLVA 412 NP+M IPF LV +L + AA +G + T + PWT+P + F T G ++ ++ Sbjct: 340 NPIMLIPFNLVPLVLVTVQYAAMKIGAVAVTTGVFIPWTLPPVISGFIVT-GHLSGSVMQ 398 Query: 413 LFNLGIATLIYLPFVVVANKAQNAID 438 + NL I ++YLPF+ + +K A + Sbjct: 399 ILNLLIGAMLYLPFMRIVDKQYRAAE 424 Lambda K H 0.326 0.141 0.423 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: 571 Number of extensions: 35 Number of successful extensions: 7 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: 452 Length of database: 439 Length adjustment: 32 Effective length of query: 420 Effective length of database: 407 Effective search space: 170940 Effective search space used: 170940 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 (21.6 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