Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= SwissProt::P37439 (477 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 349 bits (895), Expect = e-100 Identities = 204/481 (42%), Positives = 292/481 (60%), Gaps = 32/481 (6%) Query: 9 LQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAIGVA 68 LQ +G++LMLP++VLP+AG+LL +G + + V + AG ++F N+ ++FAIGVA Sbjct: 8 LQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFV-----SAAGTAIFGNLGILFAIGVA 62 Query: 69 LGFTNN-DGVSALAAVVAYGIMV---KTMAVVAP-LVLHLPAEEIAAKHLADTGVLG--- 120 +GF + +G +ALA V Y + +T + P +V LP + AAK +A G Sbjct: 63 VGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLP--DAAAKVVAQAWATGQID 120 Query: 121 ------GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFVWPP 174 GIISG I +NRF I LPEYL FF G+RFVPI +G+A + VL + + Sbjct: 121 RLEVPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAH 180 Query: 175 IGTAIQAFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFH 234 I +A+ A S A ++ +YG + R L+ GLHH+ N +G++ A G Sbjct: 181 ISSALDAASH-AVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDFGGATG---- 235 Query: 235 GDIPRYMAGDPTAG-MLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFL 293 D+ R+ AGDP AG +SG F M+GLPAA +A++H A+PE R VGG++ S A TSFL Sbjct: 236 -DLGRFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFL 294 Query: 294 TGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSK 353 TG+TEPIEF+FMF+AP+LY IHA+L G+A + +LG++ G FS GL D+++ S++ Sbjct: 295 TGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKLSTR 354 Query: 354 LWLFPIVGAGYAIVYYTVFRVLIKALDLKTPGREDTTDDAKAGAT---SEMAPALVAAFG 410 W+ VGA YA++YYT+FR I+ LDL TPGRE A AG T +E A V A G Sbjct: 355 PWMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFVKALG 414 Query: 411 GKENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVV-VAGSGVQAIFGTKSDNLKTE 469 G N+T++DAC TRLR+ VAD + VD A L LGA G++ + + Q + G +D + E Sbjct: 415 GAANLTSVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADLVAEE 474 Query: 470 M 470 + Sbjct: 475 I 475 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: 835 Number of extensions: 59 Number of successful extensions: 8 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: 560 Length adjustment: 35 Effective length of query: 442 Effective length of database: 525 Effective search space: 232050 Effective search space used: 232050 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