Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_043743857.1 AMB_RS08150 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >NCBI__GCF_000009985.1:WP_043743857.1 Length = 757 Score = 269 bits (687), Expect = 5e-76 Identities = 176/521 (33%), Positives = 260/521 (49%), Gaps = 11/521 (2%) Query: 309 NAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQSID 368 + + +L+ L +AL ++ + E S + + E + + ED L ++I Sbjct: 216 DTDAELERLKKALTGIKLALEELFSRPEM-RDGEHRDVLETYRMFAEDKGWLNRISEAIH 274 Query: 369 QGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWHY-----DV 423 G A A + + + Q+ +P L ER +D DL R+L+ L G D D+ Sbjct: 275 TGLTAEAAVQKVHDDTRARMSQITDPYLRERMHDFEDLANRLLQHLAGGDDDQRPGAADL 334 Query: 424 PAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQ 483 P GAI+ L P +L + + GL + EG ATSHVAI+AR +P + + L + Sbjct: 335 PEGAILIGRNLGPMELFDYDPKRLRGLVLEEGSATSHVAIVARALDIPVVGRVKDVLDKI 394 Query: 484 PQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVA 543 V+ D D G++ + P E A + R+ PA TR +RI + Sbjct: 395 EPLDPVICDGDNGQVFIRPPDDIRETYIDAISQRQLRQAVYARLRELPAVTRQDVRIGIH 454 Query: 544 ANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSVIIR 603 N + GADG+GL RTE F+ R + PD Q Y+ +LD K V+ R Sbjct: 455 MNAGLLLDLQHLHDSGADGIGLYRTELPFMARSSLPDVAAQTLLYKKILDQAEGKPVVFR 514 Query: 604 TIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPM 663 T+DVGGDK L Y E NP LG R IR+ RP ++ QLRALL+ + + ++ PM Sbjct: 515 TLDVGGDKVLPYWNPYEEDNPALGWRSIRITLDRPAVMRSQLRALLRAAQGRELSVMFPM 574 Query: 664 VTEVDELLYIRQRLD-ALCAELA----LTQRLELGVMIEVPAAALLAEQLAEHADFLSIG 718 + EV E + R LD L E A + RL++G M+EVPA AL + L DF+SIG Sbjct: 575 IAEVSEFVQARLILDKELERERAMGNPMPSRLKVGTMLEVPALALQLDALLPMVDFVSIG 634 Query: 719 TNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLAT 778 +NDL+Q+ A+DR + +A R D+L PA++R + A++ + VCG +A PL Sbjct: 635 SNDLTQFLFAVDRGNPRIAERYDSLAPAMVRFMRYVAAKCAQYGVTLSVCGEMAGRPLEA 694 Query: 779 PVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLL 819 LIG+GI LS+S P +G +K VR LD + TLL Sbjct: 695 MALIGVGIRHLSLSAPNIGPVKTMVRSLDIGALEAYMNTLL 735 Lambda K H 0.318 0.133 0.379 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: 1273 Number of extensions: 67 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: 838 Length of database: 757 Length adjustment: 41 Effective length of query: 797 Effective length of database: 716 Effective search space: 570652 Effective search space used: 570652 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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