Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 363 bits (933), Expect = e-105 Identities = 199/476 (41%), Positives = 291/476 (61%), Gaps = 26/476 (5%) Query: 1 MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60 M++ LQ++G++LMLP+++LPIAG+LL +G + L + H +AG +FAN+ Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDL--LNIAIIH---DAGQVIFANLA 55 Query: 61 LIFAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVL 119 +IFAIG+A+GF +N+G + LA V+ Y +M+ T+ + P + + G+L Sbjct: 56 MIFAIGIAVGFARDNNGTAGLAGVIGYLVMISTLKALDPSI--------------NMGML 101 Query: 120 GGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAI 179 GI+SG +A ++NRF IKLPEYL FF G+RFVPI++G AA+ GVV +IWPPI I Sbjct: 102 AGIVSGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGI 161 Query: 180 QTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTN-AAGQVFHGDIP 238 +F AF ++G R L+ GLHHI N G +T+ G + GD+ Sbjct: 162 NSFGTLMMESGSFGAF-VFGLFNRLLIVTGLHHILNNMAWFVFGNFTDPTTGALVTGDLS 220 Query: 239 RYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGIT 297 RY AGDP G+ ++G F ++GLPAA +A++ +A P R +GGI +S ALT+FLTG+T Sbjct: 221 RYFAGDPKGGQFMTGMFPMMIFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVT 280 Query: 298 EPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLF 357 EPIEF+FMF+AP+L+++HA+L GL+ I L + G +FS G ID I+ G S+ WL Sbjct: 281 EPIEFAFMFLAPLLFVLHALLTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLV 340 Query: 358 PIVGIGYAIVYYTIFRVLIKALDLKTPGREDATE-DAKATGTSEMAPALVAAFGGKENIT 416 VG+ YA++YY +F I+ DLKTPGRE + + + A +E A A + A GG EN+ Sbjct: 341 FPVGLAYAVIYYVVFDFCIRRFDLKTPGRETSADVEQVAVADNERAGAYIKALGGAENLI 400 Query: 417 NLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSG--VQAIFGTKSDNLKTEM 470 + AC TRLR+ + D +K LK LGA VV G G +Q + G +D + E+ Sbjct: 401 TVGACTTRLRLDMVDRNKASDTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEI 456 Score = 37.7 bits (86), Expect = 1e-06 Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 3/93 (3%) Query: 381 LKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDA-CITRLRVSVADVSKVDQAG 439 + +P E A T E A + A GG +N+ LD +TR+R+ +AD + + Sbjct: 468 VSSPAAEIDAPPPAAMATPE-AQQWLNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFD 526 Query: 440 LKKLGAAGVVVAGSGV-QAIFGTKSDNLKTEMD 471 LK LG GV G+ + G K+ L ++ Sbjct: 527 LKALGCQGVSQLDGGIWHLLIGDKAPTLSDALE 559 Lambda K H 0.325 0.140 0.422 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: 793 Number of extensions: 46 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 477 Length of database: 571 Length adjustment: 35 Effective length of query: 442 Effective length of database: 536 Effective search space: 236912 Effective search space used: 236912 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: 40 (21.6 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