Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_011386738.1 AMB_RS22220 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_000009985.1:WP_011386738.1 Length = 596 Score = 317 bits (812), Expect = 1e-90 Identities = 211/589 (35%), Positives = 312/589 (52%), Gaps = 32/589 (5%) Query: 258 VAEPVATQSSATLLRGVCASPGSAFGQVV-----QVTDPELVITEQGTGGATERAALTRG 312 V AT + + G+ S G A G + +T PEL I E A Sbjct: 10 VGRSKATARAELVRDGLGVSRGIAIGTLYLHDAGTITVPELRIPAARLDA--ECARFNEA 67 Query: 313 LLAANEALQVLQDKA------AGSAQAEIFRAHQELLEDPTLLEHAH-RLLGEGKSAAFA 365 A ++ LQDKA AG + A++++L LL R+ + +A A Sbjct: 68 SANAGRQVEQLQDKAGRLGGAAGEELGYLLDAYRQMLHGSRLLRGVEARIRNDRINAEAA 127 Query: 366 WNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWD-LPERAILIAEQL 424 V F+ + + +A R AD+ D+G+R+L+ + + LP A+++AE++ Sbjct: 128 VQQEINEIVRGFEAMEDPYLAARVADIKDIGRRLLRALTNTAYRPFTALPRNAVIVAEEM 187 Query: 425 TPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDAD 484 TP+ TA LD +V G TV GG+ H AI+AR+LGLP++ G+ + + G+QV++D Sbjct: 188 TPADTALLDPNQVAGLATVMGGSEGHTAIMARSLGLPSVLGIADLLTGVKGGEQVIIDGT 247 Query: 485 KGELHLEPN---LAEIEQLEAA--RKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASL 539 G + + P LA + AA + +VL +DV PA TRDG + + AN+ Sbjct: 248 NGLVVINPGPETLAFYRRERAAFLKARRVLSRLKDV-----PAVTRDGGRITLQANMELP 302 Query: 540 QEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVG 599 EV L G EG+GLLRSEFLY++R+ PS +EQ + +G R + VRT D G Sbjct: 303 NEVGAVLDSGAEGIGLLRSEFLYMNRDDVPSEDEQYAILKDVVERMGG-RTVTVRTFDAG 361 Query: 600 GDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLS 659 GDK + NP LGLR IRL L R LL Q AIL ++ + I++PM++ + Sbjct: 362 GDKLAPALGCTIGPNPSLGLRAIRLGLARQDLLEAQLAAILRASAHGPVRILIPMIATVG 421 Query: 660 ELHLARKILEEEALAL---GLT---ELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDL 713 EL R+++ L G++ LP+LG MIE+P AAL AD A H DFF+IGTNDL Sbjct: 422 ELRATREVMNRVIRRLRKAGVSLPDPLPRLGAMIEIPGAALSADSIAWHADFFAIGTNDL 481 Query: 714 TQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLI 773 QYTLA+DR +A+ + HPAVLRLI T +AA V VCG +A + P+L+ Sbjct: 482 VQYTLAIDRSDEAVAHLYNPLHPAVLRLIQFTTQAAQRANIPVSVCGEMAGDPRYAPLLL 541 Query: 774 GLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREAL 822 GLG+ +LS+S +P +K +R LDLA + +AR V+ ++ ++ + L Sbjct: 542 GLGLRDLSMSTSNLPVVKNRIRSLDLAAAETLARTVMEQTDSGKIGQLL 590 Lambda K H 0.318 0.133 0.371 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: 1069 Number of extensions: 45 Number of successful extensions: 5 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: 838 Length of database: 596 Length adjustment: 39 Effective length of query: 799 Effective length of database: 557 Effective search space: 445043 Effective search space used: 445043 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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