Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= SwissProt::P37439 (477 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 551 bits (1421), Expect = e-161 Identities = 285/485 (58%), Positives = 364/485 (75%), Gaps = 9/485 (1%) Query: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANF-SWLPAVVSHVMAEAGGSVFANM 59 +FK+AF LQKVGKSLMLPV+VLP+AG+LLG+G+ +F ++PA+V +M AG +FAN+ Sbjct: 1 VFKHAFGVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANL 60 Query: 60 PLIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIAAKHLADTGVL 119 PLIFAIGVALGFT NDGVS +AA + Y +M T+ V+A V + + I TGV Sbjct: 61 PLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVIAK-VEGIEPDMIMGIPSIQTGVF 119 Query: 120 GGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFVWPPIGTAI 179 GGI++G +AA+MFNR+YRI LP YLGFFAGKRFVPI++ + +I G +LS VWPPIG+AI Sbjct: 120 GGILAGGLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAI 179 Query: 180 QAFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTN-AAGQVFHGDIP 238 +AFSQWAA +P A +YGF+ER L+PFGLHHIWNVPF + G + + G+V HGDI Sbjct: 180 KAFSQWAAVSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDIT 239 Query: 239 RYMAGDPTAGMLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITE 298 R+ AGD TAG+L+G FLFKM+GLPAAAIAIWH AKPEN+ VGG+M+SAALTSFLTGITE Sbjct: 240 RFFAGDRTAGILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITE 299 Query: 299 PIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV--LSGN-SSKLW 355 PIEF+F+FVAP+LY+IHA LA A + LGMR G +FS G IDF++ L GN S+ W Sbjct: 300 PIEFAFLFVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAW 359 Query: 356 LFPIVGAGYAIVYYTVFRVLIKALDLKTPGREDTTDDAKAGATSEM---APALVAAFGGK 412 I+G YA++YY VFR +I DLKTPGRED T + +T+ + + LV AFGG+ Sbjct: 360 YVFILGPIYAVIYYGVFRFVITRFDLKTPGREDDTVETAKVSTAGVGGRSRELVLAFGGR 419 Query: 413 ENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDE 472 NI +LDACITRLR+SV + A V++ LK LGAAGVV G+GVQAIFG S+N+KT+M E Sbjct: 420 SNIDSLDACITRLRISVKNPALVNEGKLKALGAAGVVRVGNGVQAIFGPLSENMKTDMHE 479 Query: 473 YIRNS 477 Y++ + Sbjct: 480 YLKTA 484 Score = 38.5 bits (88), Expect = 6e-07 Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 2/74 (2%) Query: 399 SEMAPALVAAFGGKENITNLDA-CITRLRVSVADVAKVDQAGLKKLGAAGVVVAGSG-VQ 456 +E + AA GG NI LDA TRLRV + D +++D A LK G +G Sbjct: 522 AERVEKIRAALGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFD 581 Query: 457 AIFGTKSDNLKTEM 470 I G + NL M Sbjct: 582 LIVGLDAPNLAGAM 595 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: 891 Number of extensions: 47 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 477 Length of database: 596 Length adjustment: 35 Effective length of query: 442 Effective length of database: 561 Effective search space: 247962 Effective search space used: 247962 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