Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC
Query= CharProtDB::CH_001857 (699 letters) >NCBI__GCF_001277175.1:WP_038857764.1 Length = 499 Score = 432 bits (1112), Expect = e-125 Identities = 235/507 (46%), Positives = 327/507 (64%), Gaps = 46/507 (9%) Query: 9 LQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQIVF 68 L IGRALMLP+++LPAAG+LLA G+ +M +AG ++F Sbjct: 14 LSMIGRALMLPISLLPAAGLLLAFGDKFH-------------------LPLMMNAGGVIF 54 Query: 69 DNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAKFFTE 128 DNLPLLFA+G A+GLA+ G+A ++A + ++N+++S L G P + K Sbjct: 55 DNLPLLFAIGSAVGLASESGIAALSAAVSVFIINITISTQL---GITPEMAASGGK---- 107 Query: 129 NHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVTSIS 188 Y ++GIPTL GVFGG+I G+LAA +NRF+T++LP++LGFF+GKRFV I + Sbjct: 108 ----YAMVVGIPTLQMGVFGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFL 163 Query: 189 ALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSPFWY 248 + +LGL + +W IQ G++A S + N + FIFG++ER+LIP GLHHI+Y FWY Sbjct: 164 SFLLGLALPYVWQHIQAGIDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWY 223 Query: 249 EFFSYKSAAGEIIRGDQRIFMAQIKDGVQ-------LTAGTFMTGKYPFMMFGLPAAALA 301 F Y + G++I GDQ I+ +++GV+ AG FM G++P M+F LPAA LA Sbjct: 224 SFGDYTTQTGQVIHGDQTIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLA 283 Query: 302 IYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQ 361 +YHEA +NKK+ +GI+ SAALT FLTGITEP+EF+F+FVAPVL+ + + AGL++M M Sbjct: 284 MYHEASTKNKKIASGILFSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMY 343 Query: 362 LLNVKIGMTFSGGLIDYFLFGILPN----RTAWWLVIPVGLGLAVIYYFGFRFAIRKFNL 417 LL+ I +FS GLIDY FGILP+ +T + + VG+ +A+IYYF FRF IR+F++ Sbjct: 344 LLDAHIAKSFSAGLIDYISFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDV 403 Query: 418 KTPGREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDK 477 KTPGR D +A KT +L I+ +G +ENI + ACITRLR+ V VDK Sbjct: 404 KTPGRVDVT--ASADDKTD--AELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDK 459 Query: 478 DRLKQLGASGVLEVGNN-IQAIFGPRS 503 D L LGA GV+ VG+N IQ IFG R+ Sbjct: 460 DGLNGLGARGVVFVGDNGIQVIFGARA 486 Lambda K H 0.323 0.141 0.412 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: 965 Number of extensions: 48 Number of successful extensions: 7 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: 699 Length of database: 499 Length adjustment: 37 Effective length of query: 662 Effective length of database: 462 Effective search space: 305844 Effective search space used: 305844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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