Align PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= SwissProt::Q53922 (692 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 451 bits (1161), Expect = e-131 Identities = 265/692 (38%), Positives = 398/692 (57%), Gaps = 71/692 (10%) Query: 10 GQLQRIGKALMLPVAILPAAGILLTFGNAMHNEQILHFAPWMQHHYIQLISQIMEASGQV 69 G QR+G+AL LP+A+LP A +LL FG +L+ IS I +A G Sbjct: 5 GFFQRLGRALQLPIAVLPVAALLLRFG----QPDLLN------------ISFIAQAGG-A 47 Query: 70 IFDNLPLLFAMGTALGLA-GGDGVAGIAALVGYLIMSATMGKIAGITIDDIFSYADGAKT 128 IFDNL L+FA+G A + G A +A VGY +++ M +TI+ Sbjct: 48 IFDNLALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAM-----VTIN----------- 91 Query: 129 LGQSAKDPAHALVLGIPTLQTGVFGGIIIGALAAWCYNKFYNIQLPQFLGFFAGKRFVPI 188 P + GV GII G + YN++ I+LP FL FF GKRFVPI Sbjct: 92 ----------------PAINMGVLAGIITGLVGGAVYNRWSGIKLPDFLSFFGGKRFVPI 135 Query: 189 ITSLVAIVTGIVLSFVWPPVQDGLNNLSNFLLGKNLALTTFIFGIIERSLIPFGLHHIFY 248 T +V + +VWPPVQ+ ++ +++G AL + IFG I R LIP GLH + Sbjct: 136 ATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAG-ALGSGIFGFINRLLIPTGLHQVLN 194 Query: 249 APFWFEFGHYVNESGNLVRGDQRIWMAQYQDGVPFTAGAFTTGKYPFMMFGLPAAAFAIY 308 WF+ G + N +G + GD + A DG TAG F +G +P MMFGLP AA A+Y Sbjct: 195 TIAWFQIGEFTNAAGAVFHGDINRFYA--GDG---TAGMFMSGFFPIMMFGLPGAALAMY 249 Query: 309 RQAKPERRKVVGGLMLSAALTSFLTGITEPLEFSFLFVAPILYVAHVILAGTSFLIMHLL 368 A ERR +VGG++LS A+T+FLTG+TEPLEF F+F+AP+LY+ H IL G S + L Sbjct: 250 FAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGISLFVATAL 309 Query: 369 HVQIGMTFSGGFIDYILYGLLSWDRSNALLVIPVGIAYALIYYFLFTFLIKKLNLKTPGR 428 + G +FS G IDY+L L N ++I +G+ + +IY+ LF+ +I+ NLKTPGR Sbjct: 310 GIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIRMFNLKTPGR 369 Query: 429 EDK-------EVESK-DVSVSELPFEVLEAMGNKDNIKHLDACITRLRVEVRDKGLVDVE 480 EDK E S + +++L + A+G DN+K +DACITRLR+ V D LV+ Sbjct: 370 EDKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSALVNDA 429 Query: 481 KLKQLGASGVLEVG-NNMQAIFGPKSDQIKHDMQQIM-DGKITSPAETTVTEDGDVETAE 538 K+LGASGV+++ +Q I G K++ + +M++++ G + + A + + + + Sbjct: 430 ACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAASHSAPVAAQAVK 489 Query: 539 IVAEGGA----VIYAPITGEAVDLSEVPDKVFSAKMMGDGIAIKPETGEVVAPFDGKVKM 594 A A + +PITG+ V L +VPD+ F++K +GDG+A+KP VVAP G V Sbjct: 490 PQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVVAPAAGTVVK 549 Query: 595 IFPTKHAIGLESKDGIELLIHFGLETVKLDGEGFEILVKENDNIVLGQPLMKVDLNYIKE 654 IF T HA LE+++G E+++H G++TV L+G+GF+ LV+E + G+P++++DL ++ Sbjct: 550 IFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPILELDLEFLNA 609 Query: 655 HADDTITPIIITNAGSANIEVLH-TGKVEQGE 685 +A I+P++ +N+ + V+ TGKV G+ Sbjct: 610 NARSMISPVVCSNSDDYSALVIQATGKVVAGQ 641 Lambda K H 0.323 0.142 0.417 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: 1064 Number of extensions: 50 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 692 Length of database: 650 Length adjustment: 39 Effective length of query: 653 Effective length of database: 611 Effective search space: 398983 Effective search space used: 398983 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 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