Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_058858173.1 AS188_RS06525 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_001482365.1:WP_058858173.1 Length = 566 Score = 281 bits (719), Expect = 7e-80 Identities = 217/570 (38%), Positives = 297/570 (52%), Gaps = 41/570 (7%) Query: 273 GVCASPGSAFGQVVQVTDPELVITEQGTGGATE----RAALTRGLLAANEALQVLQDKAA 328 GVCA G G++V + P + E G A A+ R AA E L+ +A Sbjct: 8 GVCA--GRVIGELVSMPAP---VAEPAAGLALRDEAPEDAVARLQEAAAEVKAELKRRAE 62 Query: 329 GSAQ---AEIFRAHQELLEDPTLLEHAHRLLGE-GKSAAFAWNSATLATVTLFQGLGNAL 384 + + A++ ++ + D LL++A +L+ + G + A A A + LG + Sbjct: 63 AATEKDAADVLKSTALMAGDRALLKNAGKLITDRGLAPERALWEAASAYAEQMRALGGYM 122 Query: 385 IAERAADLADVGQRVLKLILGIQDSAWDLPERA---ILIAEQLTPSQTASLDTRKVLGFV 441 AERAAD+ DV R++ + G+ +PER +L AE L P+ TA+LD KVL V Sbjct: 123 -AERAADIEDVRARLVARLRGLPMPG--IPERETPFVLTAEDLAPADTATLDPAKVLALV 179 Query: 442 TVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLE 501 T AGG SH AILAR LGLPAI V LA+G +V +D GE+ EP E E + Sbjct: 180 TSAGGPQSHTAILARNLGLPAIVAARG-VEELADGTEVFVDGATGEVRTEPGAEERELVA 238 Query: 502 AARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFL 561 + + R D DG V + ANV + ++ A G +GVGLLR+EF Sbjct: 239 SWERAAAARSDFDGR-----GVLADGTEVPLYANVGTAEDARTAAAAGAQGVGLLRTEFC 293 Query: 562 YLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRG 621 +L R PS EEQ YTAI A E+ +VVRTLD G DKPL ++ AE NP LG+RG Sbjct: 294 FLGRGEEPSVEEQVEQYTAIFAAF-EEKKVVVRTLDAGADKPLPFLTDTAEPNPALGVRG 352 Query: 622 IRLCLERPQLLREQFRAILAS--AGFARLHIMLPMVSLLSELHLARKILEEEALALGLTE 679 R P +L Q AI + A A + +M PM+S E AR A A GL Sbjct: 353 YRTDRSVPGVLARQLEAIARADEATAAEVWVMAPMISAAEE---ARDFAAMAATA-GL-R 407 Query: 680 LPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVL 739 +P G+M+E PSAA+ AD HV+F S+GTNDLTQYT+A DR LA + + PAVL Sbjct: 408 VP--GVMVETPSAAVTADQILRHVEFVSLGTNDLTQYTMAADRMLGSLAELNNPWQPAVL 465 Query: 740 RLIATTVKAAH------AHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKAT 793 R++ TV+ A A + VGVCG A++ VL+GLGV LS+S + + A Sbjct: 466 RMVRLTVEGARRAEAEGAGRRNVGVCGEAAADPALAVVLVGLGVHTLSMSPRALSPVAAV 525 Query: 794 VRELDLADCQIIARQVLGLEEAAEVREALR 823 +R +DLA + +A + AAE A+R Sbjct: 526 LRSVDLATARSLAELAVEQATAAEAAAAVR 555 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: 989 Number of extensions: 52 Number of successful extensions: 7 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: 566 Length adjustment: 39 Effective length of query: 799 Effective length of database: 527 Effective search space: 421073 Effective search space used: 421073 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 24 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