Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_043743857.1 AMB_RS08150 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >NCBI__GCF_000009985.1:WP_043743857.1 Length = 757 Score = 263 bits (671), Expect = 4e-74 Identities = 192/593 (32%), Positives = 282/593 (47%), Gaps = 18/593 (3%) Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVA 295 E E LA+LL G E V +V V+ + + GV + G G V Sbjct: 149 ETLETVAMVLAELLVSG--ELVNRAELVP--VDGNALLPLRMEGVKLNGGVGVGVAVLHR 204 Query: 296 ERTLEMPEFAADQQLERESLERALMHATQALQRL--RDNAAGEAQADIFKAHQELLEDPS 353 R A D E E L++AL AL+ L R D+ + ++ ED Sbjct: 205 PRITIQRLVAEDTDAELERLKKALTGIKLALEELFSRPEMRDGEHRDVLETYRMFAEDKG 264 Query: 354 LLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVP 413 L + I G +A A + T + L ER D D+ R+L+ + G Sbjct: 265 WLNRISEAIHTGLTAEAAVQKVHDDTRARMSQITDPYLRERMHDFEDLANRLLQHLAGGD 324 Query: 414 D----GVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAV 469 D G +LP+ AILI L P + D ++ G G ATSHVAI+ARAL +P V Sbjct: 325 DDQRPGAADLPEGAILIGRNLGPMELFDYDPKRLRGLVLEEGSATSHVAIVARALDIPVV 384 Query: 470 CGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAV 529 + + + V+ D D G++ + P + E Q++ R AV Sbjct: 385 GRVKDVLDKIEPLDPVICDGDNGQVFIRPPDDIRETYIDAISQRQLRQAVYARLRELPAV 444 Query: 530 TRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA- 588 TR + N L + + GA+GIGL R+E + RS P Q Y I Sbjct: 445 TRQDVRIGIHMNAGLLLDLQHLHDSGADGIGLYRTELPFMARSSLPDVAAQTLLYKKILD 504 Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSS 648 +A G + +V RTLDVGGDK L Y E NP LG R IR+ L+RP ++R Q RA+L + Sbjct: 505 QAEG--KPVVFRTLDVGGDKVLPYWNPYEEDNPALGWRSIRITLDRPAVMRSQLRALLRA 562 Query: 649 AGLARLHIMLPMVSQLSELRLARLMLEEE-----ALALGLRELPKLGIMIEVPAAALMAD 703 A L +M PM++++SE ARL+L++E A+ + K+G M+EVPA AL D Sbjct: 563 AQGRELSVMFPMIAEVSEFVQARLILDKELERERAMGNPMPSRLKVGTMLEVPALALQLD 622 Query: 704 LFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVG 763 P VDF SIG+NDLTQ+ A+DR +PR+A + DS P+++R + +G + Sbjct: 623 ALLPMVDFVSIGSNDLTQFLFAVDRGNPRIAERYDSLAPAMVRFMRYVAAKCAQYGVTLS 682 Query: 764 VCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVL 816 VCG +A L L+G+G+ LS+S P I +K +R +++ +A + +L Sbjct: 683 VCGEMAGRPLEAMALIGVGIRHLSLSAPNIGPVKTMVRSLDIGALEAYMNTLL 735 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: 1222 Number of extensions: 50 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: 844 Length of database: 757 Length adjustment: 41 Effective length of query: 803 Effective length of database: 716 Effective search space: 574948 Effective search space used: 574948 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: 55 (25.8 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