Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC
Query= BRENDA::P09323 (648 letters) >NCBI__GCF_001277175.1:WP_038857764.1 Length = 499 Score = 318 bits (816), Expect = 3e-91 Identities = 193/494 (39%), Positives = 270/494 (54%), Gaps = 46/494 (9%) Query: 10 LGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKDSA 69 +GRAL LPI++LP A LLL FG D ++ + AGG IFDNL L+FAIG A + +S Sbjct: 17 IGRALMLPISLLPAAGLLLAFG--DKFHLPLMMNAGGVIFDNLPLLFAIGSAVGLASES- 73 Query: 70 GAAALAGAVGYFVLT-------------------KAMVTINPEINMGVLAGIITGLVGGA 110 G AAL+ AV F++ AMV P + MGV G+I+G++ Sbjct: 74 GIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQMGVFGGLISGILAAW 133 Query: 111 AYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAG 170 YNR+ ++LP+FL FF GKRFV IA F +L YVW +Q I A + Sbjct: 134 CYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAGIDALSVIVNGDN 193 Query: 171 -ALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGD-----------INR 218 A + IFG + R LIP GLH + W+ G++T G V HGD + Sbjct: 194 QAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGDQTIWFKMLEEGVKS 253 Query: 219 FYAGD-GTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVT 277 F + AG FM G FP+M+F LP A LAMY A + + + G+L S A+T FLTG+T Sbjct: 254 FSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGILFSAALTCFLTGIT 313 Query: 278 EPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAAS--- 334 EP+EF F+F+AP+LY+ +A++ G++ LL H SFSAG IDY LP+ + Sbjct: 314 EPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDYISFGILPSFNGYQ 373 Query: 335 QNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLAT 394 + +++G+ IY+ F VIR F++KTPGR D VT A+ T+ +LA Sbjct: 374 THYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRVD-----VTASADDKTD---AELAG 425 Query: 395 NYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAK 454 N + +GG +N+ ++ ACITRLRL VA V+ LGA GVV + IQVI GA+ Sbjct: 426 NIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQVIFGAR 485 Query: 455 AESIGDAMKKVVAR 468 A+ I ++ + + Sbjct: 486 AQFIAQSLSGMTGK 499 Lambda K H 0.324 0.139 0.408 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: 777 Number of extensions: 40 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: 648 Length of database: 499 Length adjustment: 36 Effective length of query: 612 Effective length of database: 463 Effective search space: 283356 Effective search space used: 283356 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: 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