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 AO356_07335 AO356_07335 PTS fructose transporter subunit IIA
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07335 Length = 954 Score = 462 bits (1189), Expect = e-134 Identities = 287/670 (42%), Positives = 383/670 (57%), Gaps = 21/670 (3%) Query: 177 RARVAHHGGLHARPAALLRKTAQGFSSQAELHFA-GQVASVD--SLVGIMGLGVAEQDEV 233 R +A+ GLHARPA +L + A+ F + + GQ ++V SL ++ LG + Sbjct: 286 RIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVL 345 Query: 234 EVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLA--------G 285 E I + AL ALLAA+ + P AP E LA Sbjct: 346 EFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQA 405 Query: 286 VCASPGLASGP--LARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGG 343 V A+PG+A GP + L AI P E + L AL +VR D+QG +++A+ Sbjct: 406 VAAAPGIAIGPAHIQVLQAIDYPLRGESAAIERERL--QNALNQVRSDIQGLIERAKAKA 463 Query: 344 DENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAER 403 IF H +L+DP L D D + G A AW I+A + +AL + LLAER Sbjct: 464 IRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAER 520 Query: 404 ANDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATS 463 A DLRD+ +RVL L G P I+ E+ PSD+A L AG+ A GGAT+ Sbjct: 521 AADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATA 580 Query: 464 HVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREE 523 H AI+AR+ G+P LV GA +L L G ++LD +GRL + PDA L++ A + E Sbjct: 581 HSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQR-AKEERDTRE 639 Query: 524 QRRRQQADAQRE-ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAA 582 QR + A+ + E ALTRDG +E+ AN+ A A GA+G+GLLRTE +F+ A Sbjct: 640 QRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQA 699 Query: 583 PDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARP 642 PDE Q Y++VLD + R +++RT+DVGGDK L Y P+ EENP LG+RGI L RP Sbjct: 700 PDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRP 759 Query: 643 ELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEV 702 ++++ QLRALLR RI+ PMV VDE R R L ++ + L +LG+MIEV Sbjct: 760 QVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMIEV 818 Query: 703 PSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGA 762 PSAALLA LA+ DF S+GTNDL+QY LA+DR H L+ + D LHPA+L+LI T A Sbjct: 819 PSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAA 878 Query: 763 ARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQAL 822 HG+WVGVCG LA+DPLA PVLVGLGV+ELSV + E+K RVR+L A+ + AQA Sbjct: 879 HAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQAA 938 Query: 823 LDLGSARAVR 832 L +GSA VR Sbjct: 939 LAVGSADDVR 948 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: 1923 Number of extensions: 109 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 842 Length of database: 954 Length adjustment: 43 Effective length of query: 799 Effective length of database: 911 Effective search space: 727889 Effective search space used: 727889 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: 56 (26.2 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