Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate 6937494 Sama_1650 phosphotransferase system, enzyme I (RefSeq)
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__SB2B:6937494 Length = 567 Score = 299 bits (766), Expect = 3e-85 Identities = 202/569 (35%), Positives = 294/569 (51%), Gaps = 21/569 (3%) Query: 285 GVCASPGLASGPLARLGAISLPADDGR---HRPEEQHLALDQALQRVRDDVQGSLQQARL 341 G+ PG+ G P D R +Q LD L R++ + SLQ L Sbjct: 5 GIAIKPGVTFGEALHFNTGHKPLDYRILPIKRIPQQLSRLDGGLARLKQQLSASLQA--L 62 Query: 342 GGDENEAAIFSAHLALLEDPGL-LDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLL 400 + A+ A L L+DP L AD + A + R Q L+AL + L Sbjct: 63 DSQSDAYALVEADLLYLDDPDLRAHIADTITQLQFSACVSIERVFAHQASELEALDDPYL 122 Query: 401 AERANDLRDLEKRVLRVLLG----DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCM 456 A+RA D+R L KR+++ + G + L+VP I+ A +I+P++ A L AG+ + Sbjct: 123 AQRAEDVRSLGKRLIQAVFGHPGQEPGKLKVPT--ILLADDISPAEFAVLPLENVAGIVL 180 Query: 457 AEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVAL 516 GG TSH AILAR+ G+P L++ L + G Q+ +D G L +P+ LE L Sbjct: 181 KSGGLTSHTAILARAAGIPALLSCPYSELGINNGDQLAIDGDAGALYRNPEGGTLE--LL 238 Query: 517 QVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEF 574 + + + R+Q D R+ A+T+DG I + ANV + + + GADG+GLLRTEF Sbjct: 239 RQHEASARLAREQLDQYRDKPAMTQDGHEISLLANVGNLNDVLKVSGLGADGIGLLRTEF 298 Query: 575 LFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRG 634 + + PDE Q Y + + A+ R + IRT+D+G DK L L EENPALGLRG Sbjct: 299 MLMHSATLPDERAQYQLYSDAIHALEGRVLTIRTLDIGADKELPCLCQVKEENPALGLRG 358 Query: 635 IHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLP 694 I A P+LL QLRA+LR R++ PMV++V+EL A+ L +L E Sbjct: 359 IRYTLANPQLLKTQLRAVLRAANHGHVRLMFPMVNQVEELDAVLALLETCRRELDDEEKG 418 Query: 695 ----ELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPA 750 LG+++E P+A L + DF+SIGTNDL+QYA+A DR + LA AL PA Sbjct: 419 FGDISLGIVVETPAAVLNLPAMLPMLDFVSIGTNDLTQYAMAADRGNPCLARDYPALSPA 478 Query: 751 LLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQL 810 +LRLI+ T A V +CG + SDP P+L+GLG +ELSV + E+K + + Sbjct: 479 VLRLISMTLQSARSQDVKVSLCGEMGSDPRLVPLLIGLGFDELSVNVGAMLEVKAAICRQ 538 Query: 811 DAAECRRHAQALLDLGSARAVRDACLQHW 839 + C + A L + + DAC+ + Sbjct: 539 EFDRCTQLAGRAL-MADRLSELDACISSY 566 Lambda K H 0.319 0.136 0.390 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: 1093 Number of extensions: 44 Number of successful extensions: 3 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: 842 Length of database: 567 Length adjustment: 39 Effective length of query: 803 Effective length of database: 528 Effective search space: 423984 Effective search space used: 423984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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