Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_086509381.1 BZY95_RS07800 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >NCBI__GCF_002151265.1:WP_086509381.1 Length = 963 Score = 489 bits (1258), Expect = e-142 Identities = 323/726 (44%), Positives = 414/726 (57%), Gaps = 49/726 (6%) Query: 139 DSGLVACAQPVLRLSLGDPRTVVAQEEGE--ALFSKPVHLPNPNGLHARPAAVFAQAAK- 195 DSG A L D TV+A+ GE A ++ + N +GLHARPA QAA+ Sbjct: 254 DSGAAA------ELPSADAATVLARLAGESAAAHTRLARVLNAHGLHARPAKQLVQAARE 307 Query: 196 -GFAASICLHKQQDSA-NAKSLVAIMALQTVHGDALQVSAVGEDAELAISTLAQLLADGC 253 G + L + +A +A SL ++ L G L SA GE A+ A+ + + +ADG Sbjct: 308 QGLPIQVRLAEGGGAAVSASSLTKVINLGARRGQQLLFSAEGEGAQQALDAVCRAVADGL 367 Query: 254 GEAVTPV----------AVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLEMPE 303 GE V P A APV + GV AS G A + + PE Sbjct: 368 GEHVLPFDESRERSMPQADAAPVEPLPDDVPH--PGVAASPGLAIAPAFVLQTPRFDYPE 425 Query: 304 FAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIA 363 AAD ++ L +AL L+ L A G A I H+E+L DP L E A+ I Sbjct: 426 RAADPAEQQRRLRQALAEGAAQLEALVRQARGGEVAQILSMHEEMLTDPELFEAAREGIQ 485 Query: 364 EGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELPDQA 423 EG+SA AW A E A + L LLAERA DL DVG+RVL ++ V +LP+ Sbjct: 486 EGRSAESAWWEAIETAAHAQEMLADRLLAERAADLRDVGRRVLGVLCEV-----QLPEPP 540 Query: 424 ----ILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSL 479 IL+ + + PS A LDT +V G T GGAT+H AILARALG+PAV G +VL+L Sbjct: 541 ETPYILVTDDIGPSDVARLDTQRVRGLLTARGGATAHSAILARALGIPAVVGAGERVLTL 600 Query: 480 ASGTRVLLDADKGELHLDPAVSVIEQLHAK-RQQQRQRHQHELENAARA-AVTRDGHHFE 537 A G ++LD ++G + PA S + A+ R +R+R + E A A A TRDGH E Sbjct: 601 AGGQELILDGERGRVI--PAPSAERRASAEQRLAERERREAEAWQARFAPAQTRDGHRVE 658 Query: 538 VTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNL 597 V AN+ + A A+ GAEGIGLLR+EFL+ + P Q Y AL R L Sbjct: 659 VAANLGNTAHAADAVERGAEGIGLLRTEFLFMAHAREPDLATQIEEYREALDAL-EGRPL 717 Query: 598 VVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLAR---- 653 V RTLDVGGDKPL Y P+ E NPFLG+RGIRL L RP++L Q RA+L +A A Sbjct: 718 VARTLDVGGDKPLPYWPVPKEDNPFLGLRGIRLSLTRPEVLETQLRALLMAAAPAASEAA 777 Query: 654 -----LHIMLPMVSQLSELRLARLMLE---EEALALGLRELPKLGIMIEVPAAALMADLF 705 L IMLPMV + E R R + E +E A +LG+MIEVP+AAL+A Sbjct: 778 DKPRPLRIMLPMVKDVGEFRATRAIFERLLDEIPAAERATDVQLGVMIEVPSAALLASAL 837 Query: 706 APEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVC 765 A EVDFFS+GTNDLTQYTLA+DRDHP L++QAD HP+VLRLI TV AAHAHGKWVGVC Sbjct: 838 AAEVDFFSVGTNDLTQYTLAIDRDHPELSAQADGLHPAVLRLIEMTVAAAHAHGKWVGVC 897 Query: 766 GALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVR 825 G LAS+TLAVP+L+GLGVDELSVS +P +KA +RE +L++ +A A L ++E VR Sbjct: 898 GELASDTLAVPVLVGLGVDELSVSARQVPLVKARLREFDLAEARAQAQLALAQATSEAVR 957 Query: 826 EALSVQ 831 +AL + Sbjct: 958 DALEAR 963 Lambda K H 0.318 0.132 0.370 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: 1755 Number of extensions: 74 Number of successful extensions: 8 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: 844 Length of database: 963 Length adjustment: 43 Effective length of query: 801 Effective length of database: 920 Effective search space: 736920 Effective search space used: 736920 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: 56 (26.2 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