Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 295 bits (756), Expect = 2e-84 Identities = 170/452 (37%), Positives = 257/452 (56%), Gaps = 20/452 (4%) Query: 23 LPAAGLLLRFGDKDLLNIP-----IIKDAGGVVFDNLPLIFAVGVAIGLAGGEGVAGLAA 77 +PAAG++L + +P ++ G ++F +P++FAV VAIG +G+A A Sbjct: 1 MPAAGVMLGLTVSPIPFMPEVLTVLMLAVGKLIFAIMPILFAVAVAIGFCRDQGIAAFTA 60 Query: 78 VIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAYLYKRFSSIELHPV 137 V GY ++T TL + L L +D G+ GG++IG + + + I L + Sbjct: 61 VFGYGVMTATLAALADLYQLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPAI 120 Query: 138 LGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSLIADSTVGLFF--YATIYR 195 FF G+R ++ ++ +G I + VWP + I S + F Y + R Sbjct: 121 FSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYGALER 180 Query: 196 LLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCL 255 LLIP GLHHI+ PFY +G+Y V G++ R+ AGDP AG + G + ++ L Sbjct: 181 LLIPLGLHHIWNAPFYLEVGQY-QLQNSEVVRGEVARYLAGDPQAGN-LAGGYLIKMWGL 238 Query: 256 PAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGV 315 PA ALAI A P ++ ++G+M+SAA S LTG+TEP+EF+F+FVAP L+LI+ +L+G+ Sbjct: 239 PAAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGL 298 Query: 316 IFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTN-GWVVIPVGIVFAFIYYYLFRFAILKWN 374 + VC + + H FS G +D+ L + LS N GW V +G + A IYY LFR +IL +N Sbjct: 299 AYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVF-LGPLTAVIYYLLFRGSILAFN 357 Query: 375 LKTPGR-ETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQV 433 LKTPGR E DE P + ++ ALGG++NI L+AC+TRLR++VH P V Sbjct: 358 LKTPGRLEPDE--------PHGAKESLRAIIAALGGRENIVELNACLTRLRLSVHSPELV 409 Query: 434 CKDELKRLGAVGVLEVNNNFQAIFGTKSDALK 465 K L +LGA GV+ + Q ++GTK++ L+ Sbjct: 410 NKVRLSQLGAKGVIVMGKGVQVVYGTKAETLR 441 Lambda K H 0.324 0.142 0.421 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: 679 Number of extensions: 37 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: 631 Length of database: 452 Length adjustment: 35 Effective length of query: 596 Effective length of database: 417 Effective search space: 248532 Effective search space used: 248532 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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