Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_089136332.1 CES79_RS03595 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >NCBI__GCF_002217945.1:WP_089136332.1 Length = 573 Score = 311 bits (798), Expect = 5e-89 Identities = 181/514 (35%), Positives = 286/514 (55%), Gaps = 11/514 (2%) Query: 315 RLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSA-AP 373 R+ AL+ ++ ++A+ D AIF AH+A+L DP ++ D I A Sbjct: 43 RVHQALSVSVEDLKAIQDNAKGSLDEDTLAIFDAHIAILSDPEMIKQIDQEINDKKVNAE 102 Query: 374 HAWSR-SIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQFDVAA---GAIVA 429 A ++ + D + + + ERA D++D+ +RVL LLG+ D+AA I+ Sbjct: 103 QALTKVTTDFANTLAAMTDNQYMQERAADVKDVSKRVLSHLLGKKLP-DLAAIDSPVIIV 161 Query: 430 AQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVV 489 A E+TPSD Q++ + + G+ GG TSH AI++R G+P +V G+ + G+ V+ Sbjct: 162 AHEVTPSDTSQMNKKFIKGMITDLGGRTSHSAIMSRTLGIPAVVGAGEATQKIKNGEVVI 221 Query: 490 LDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSA 549 LD G P +Q RA+ L P+ + DG E E+A+N+ + A Sbjct: 222 LDGLNGEAISNPNETETKHYQQLAQSFEQQRAEWAKLVDAPSISADGKEFEIASNIGTPA 281 Query: 550 EAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGD 609 + + + G+D VGL RTEFL++D + P E++Q +AY+ V EAM KPV+IRT+D+GGD Sbjct: 282 DMDDVVKVGSDAVGLFRTEFLYMDSSSLPTEDDQFEAYKQVTEAMNGKPVVIRTMDIGGD 341 Query: 610 KQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDEL 669 K L+YLPLP E NP LG R IR++ R + QLRAL++ + RI+ PM+ +DE Sbjct: 342 KPLNYLPLPEEMNPFLGYRAIRISLDRQSIFRTQLRALIRASKFGQLRIMFPMIATLDEF 401 Query: 670 -----LHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQY 724 + ++ + G+ + +LG+M+E+PAAA+ AE A+ DF SIGTNDL QY Sbjct: 402 RKAKAIFTEEKKKLQVDDPGIGDDIKLGIMIEIPAAAIFAEAFAKEVDFFSIGTNDLIQY 461 Query: 725 TLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLG 784 + A DR + ++ +PALL+LI A + G+ +CG +A D +A P+L+G+G Sbjct: 462 SFAADRGNESVSYLYQPYNPALLKLIKHVIDAAHQEGKIAAMCGEMAGDAVALPLLMGMG 521 Query: 785 VRELSVSPPQIGEIKDRVRHLDAAQCARLSNELL 818 + E S+S + + ++ L+ +CA L N +L Sbjct: 522 LDEYSMSSSSVLRTRSTMKTLNTEKCAELVNHVL 555 Lambda K H 0.319 0.134 0.386 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: 851 Number of extensions: 27 Number of successful extensions: 3 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: 837 Length of database: 573 Length adjustment: 39 Effective length of query: 798 Effective length of database: 534 Effective search space: 426132 Effective search space used: 426132 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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