Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate BWI76_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__Koxy:BWI76_RS27570 Length = 363 Score = 254 bits (650), Expect = 2e-72 Identities = 135/363 (37%), Positives = 206/363 (56%), Gaps = 19/363 (5%) Query: 22 VKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVAGLTIMVPI 81 +K+ L+TG+S+MIP + GI +A+ +G T V E TG+ W L QIG G+ ++VP+ Sbjct: 12 IKKHLLTGISWMIPLIVAAGICIALGQVLGGTN-VGEKTGTIPWMLNQIGGWGMGLIVPL 70 Query: 82 LGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAG 141 + IAY+IADRPG APG ++ ++ G+ G++G ++ G L G Sbjct: 71 ICAAIAYSIADRPGFAPGLIVGFVC-----------------GQIHTGFIGGMLGGFLVG 113 Query: 142 YVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQ 200 Y K+ + +P+ +Q +MP++++PV + + +M+ ++G P+A + L L+SMQ Sbjct: 114 YTVLALKHYIRLPKSMQGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQ 173 Query: 201 GGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLALS 260 GG ++G ILG M FD GGPVNK +FA GL+ +Y P A +G +IPP G+ LS Sbjct: 174 GGSRFLLGAILGAMATFDFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLS 233 Query: 261 NFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMAL 320 + HKY E K+ +G+ ITEG IP AA D LRV+ + V SAV G M Sbjct: 234 FLLTRHKYTRAEREALKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTW 293 Query: 321 GVTMPAPHGGIFVVLLSNQPLAFLGSILLGSLVTAVVATVIKPDFEDRVDTGAETSSTQP 380 GV P PHGG+FVV L PL F S+ +G+++ V+ ++ K +R + E + + Sbjct: 294 GVESPVPHGGMFVVPLFTHPLLFCLSLAIGTVICGVMLSLWKKPVTERDEEFDELNDQKV 353 Query: 381 TDD 383 DD Sbjct: 354 KDD 356 Lambda K H 0.322 0.139 0.399 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: 521 Number of extensions: 35 Number of successful extensions: 4 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: 383 Length of database: 363 Length adjustment: 30 Effective length of query: 353 Effective length of database: 333 Effective search space: 117549 Effective search space used: 117549 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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