Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= SwissProt::P37439 (477 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 277 bits (708), Expect = 7e-79 Identities = 182/510 (35%), Positives = 269/510 (52%), Gaps = 53/510 (10%) Query: 10 QKVGKSLMLPVSVLPIAGILLGVGSANFSW-----LPAVVSHV-------MAEAGGSVFA 57 Q++GK+ MLPV++L GI+LG+GS+ S +P + + V M++ G F+ Sbjct: 16 QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFAFS 75 Query: 58 NMPLIFAIGVALGFTN-NDGVSALAAVVAYGIMVKTM-----------AVVAPLVLHLPA 105 +P++F I + LG N GV+A A + Y +M + A ++ Sbjct: 76 FLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKANNI 135 Query: 106 EEIAAKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTG 165 + I DTG+LG +I+G I + RF+ I+LP+ L FF G RFVPIIS L G Sbjct: 136 QSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGLVG 195 Query: 166 VVLSFVWPPIGTAIQAFSQWAAYQNPVVAFG--IYGFIERCLVPFGLHHIWNVPFQM-QI 222 +V+ VWP I N FG ++G ER L+PFGLHHI + Sbjct: 196 LVIPLVWPIFAMGISGLGHMI---NSAGDFGPMLFGTGERLLLPFGLHHILVALIRFTDA 252 Query: 223 GEYTNAAGQVFHGDIPRYMAG-----------DPTAGMLSGGFLFKMYGLPAAAIAIWHS 271 G GQ G + + A T + G + GLP AA+A++H Sbjct: 253 GGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHC 312 Query: 272 AKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGM 331 A+PENR K+ G++IS + + G TEP+EF F+FVAP+LY+IHA+L GL F + +LG+ Sbjct: 313 ARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGV 372 Query: 332 RDGTSFSHGLIDFIV---LSGNSSKLWLFPIVGAGYAIVYYTVFRVLIKALDLKTPGRE- 387 G + +IDF+V L G S+K ++ P+V A + +VYY +FR I +LKTPGR+ Sbjct: 373 TIGNT-DGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRDS 431 Query: 388 ---DTTDDAKAGATSEM---APALVAAFGGKENITNLDACITRLRVSVADVAKVDQAGLK 441 + + A AGA + PA++ A GG +NI +LD CITRLR+SV D++ V+ LK Sbjct: 432 EVASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQALK 491 Query: 442 KLGAAGVVVAGS-GVQAIFGTKSDNLKTEM 470 A GVV +Q + G + ++K EM Sbjct: 492 DNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 Lambda K H 0.325 0.140 0.421 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: 803 Number of extensions: 52 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: 477 Length of database: 530 Length adjustment: 34 Effective length of query: 443 Effective length of database: 496 Effective search space: 219728 Effective search space used: 219728 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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