Align PTS system N,N'-diacetylchitobiose-specific EIIC component; EIIC-Chb; IIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIC component (characterized)
to candidate BWI76_RS22405 BWI76_RS22405 PTS cellobiose transporter subunit IIC
Query= SwissProt::P17334 (452 letters) >FitnessBrowser__Koxy:BWI76_RS22405 Length = 440 Score = 216 bits (549), Expect = 2e-60 Identities = 144/458 (31%), Positives = 242/458 (52%), Gaps = 44/458 (9%) Query: 2 SNVIASLEKVLLPFAVKIGKQPHVNAIKNGFIRLMPLTLAGAMFVLI------NNVFLSF 55 + +IA +E+ + P A IG+Q +V +I++GFI +P + G+ ++ + F Sbjct: 6 AKLIAVIEQKITPMAGAIGQQKYVTSIRDGFITALPFMIVGSFLLVFIFPPFSPDTTWGF 65 Query: 56 GEGSFFYSLGIRLDASTIETLNGLKGIGGNVYNGTLGIMSLMAPFFIGMALAEERKVDAL 115 +SL R DA + +N ++G+M+L I +LA+ +D+L Sbjct: 66 ARAWLQFSLDHR-DALMLP------------FNFSMGVMTLFIAVGIAASLAKHHNLDSL 112 Query: 116 AAGLLSVAAFMTVT-PYSVGEAYAVGANWLGGANIISGIIIGLVVAEMFTFIVRRNWVIK 174 AG+LS+ +F+ V P G+ + + G I + I++ + E++ F+ R N I+ Sbjct: 113 TAGMLSLMSFLLVAAPLKDGQ---ISTAYFSGQGIFTAILVAIYSTELYAFLKRHNITIR 169 Query: 175 LPDSVPASVSRSFSALIPGF-IILSVMGIIAWALNTWGTNFHQIIMDTISTPLASLGSVV 233 LP VPA V+RSF LIP I+L++ + + G + IM + +A+ ++ Sbjct: 170 LPPEVPAGVARSFEILIPVLAIVLTLHPLNLFIEAQLGMIIPEAIMSLVKPLVAASDTLP 229 Query: 234 GWAYVIFV-PLLWFFGIHGALALTALDNGIMTPWALENIATYQQYGSVEAALAAGKTF-H 291 + V +LWF GIHGAL +T GIM P+ + N++ Q AA+AAG H Sbjct: 230 AILLSVLVCQVLWFAGIHGALIVT----GIMNPFWMANLSINQ------AAMAAGTAIPH 279 Query: 292 IWAKPMLDSFIFLGGSGATLGLILAIFIASRRADYRQVAKLALPSGIFQINEPILFGLPI 351 I+ + D ++ +GG G+TL L L + + S+ R + ++ + G+F INEPILFG PI Sbjct: 280 IYVQGFWDHYLLIGGVGSTLPLALML-LRSKAVHLRTIGRMGVVPGVFNINEPILFGAPI 338 Query: 352 IMNPVMFIPFVLVQPILAAITLAAYYMGIIPPVTNIAPWTMPTGLGAFFNTNGSVAALLV 411 IMNP+ F+PFVLV I A + A + ++ V ++ PWT P +GA + N S + +++ Sbjct: 339 IMNPLFFLPFVLVPMINATLAYFALKLDLVSRVVSMTPWTTPAPIGASWAANWSFSPVIM 398 Query: 412 ALFNLGIATLIYLPFVVVANKAQNAIDKEESEEDIANA 449 L + A ++YLPF+ A +K+ E++ ANA Sbjct: 399 CLICMATAMVMYLPFL-------KAYEKQLLEQEHANA 429 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: 554 Number of extensions: 33 Number of successful extensions: 6 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: 440 Length adjustment: 32 Effective length of query: 420 Effective length of database: 408 Effective search space: 171360 Effective search space used: 171360 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