Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 6937494 Sama_1650 phosphotransferase system, enzyme I (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__SB2B:6937494 Length = 567 Score = 291 bits (746), Expect = 5e-83 Identities = 199/571 (34%), Positives = 293/571 (51%), Gaps = 27/571 (4%) Query: 277 LRGVCASAGSAFGYVVQ--VAERTLE---MPEFAADQQLER-----ESLERALMHATQAL 326 + G+ G FG + + L+ +P QQL R L++ L + QAL Sbjct: 3 VNGIAIKPGVTFGEALHFNTGHKPLDYRILPIKRIPQQLSRLDGGLARLKQQLSASLQAL 62 Query: 327 QRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKS 385 D A +AD+ L+DP L I + + SA + A+ ++ Sbjct: 63 DSQSD-AYALVEADLL-----YLDDPDLRAHIADTITQLQFSACVSIERVFAHQASELEA 116 Query: 386 LGSTLLAERALDLMDVGQRVLKLILGVPD---GVWELPDQAILIAEQLTPSQTAALDTGK 442 L LA+RA D+ +G+R+++ + G P G ++P IL+A+ ++P++ A L Sbjct: 117 LDDPYLAQRAEDVRSLGKRLIQAVFGHPGQEPGKLKVP--TILLADDISPAEFAVLPLEN 174 Query: 443 VLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSV 502 V G GG TSH AILARA G+PA+ P L + +G ++ +D D G L+ +P Sbjct: 175 VAGIVLKSGGLTSHTAILARAAGIPALLSCPYSELGINNGDQLAIDGDAGALYRNPEGGT 234 Query: 503 IEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLL 562 +E L R + + + A+T+DGH + ANV +L + + LGA+GIGLL Sbjct: 235 LELLRQHEASARLAREQLDQYRDKPAMTQDGHEISLLANVGNLNDVLKVSGLGADGIGLL 294 Query: 563 RSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPF 622 R+EF+ + P Q YS AL R L +RTLD+G DK L + E NP Sbjct: 295 RTEFMLMHSATLPDERAQYQLYSDAIHAL-EGRVLTIRTLDIGADKELPCLCQVKEENPA 353 Query: 623 LGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALG 682 LG+RGIR L PQLL+ Q RA+L +A + +M PMV+Q+ EL +LE L Sbjct: 354 LGLRGIRYTLANPQLLKTQLRAVLRAANHGHVRLMFPMVNQVEELDAVLALLETCRRELD 413 Query: 683 LRELP----KLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQAD 738 E LGI++E PAA L P +DF SIGTNDLTQY +A DR +P LA Sbjct: 414 DEEKGFGDISLGIVVETPAAVLNLPAMLPMLDFVSIGTNDLTQYAMAADRGNPCLARDYP 473 Query: 739 SFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKA 798 + P+VLRLI+ T+++A + V +CG + S+ VPLL+GLG DELSV+V + +KA Sbjct: 474 ALSPAVLRLISMTLQSARSQDVKVSLCGEMGSDPRLVPLLIGLGFDELSVNVGAMLEVKA 533 Query: 799 AIREVELSDCQAIAHQVLGLESAEQVREALS 829 AI E C +A + L + ++ +S Sbjct: 534 AICRQEFDRCTQLAGRALMADRLSELDACIS 564 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: 989 Number of extensions: 41 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: 844 Length of database: 567 Length adjustment: 39 Effective length of query: 805 Effective length of database: 528 Effective search space: 425040 Effective search space used: 425040 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