Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >FitnessBrowser__azobra:AZOBR_RS18900 Length = 766 Score = 269 bits (687), Expect = 5e-76 Identities = 195/586 (33%), Positives = 279/586 (47%), Gaps = 24/586 (4%) Query: 242 AALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIPL 301 A + A L A VN A+ P R L+G A GL G LA I Sbjct: 165 AMVVAELVAQGELVNPQEVASTGDPALLPAR------LSGTSLASGLAMG----LAVIHR 214 Query: 302 PEDTGKH----NAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDP 357 P+ T + +AE +L L+ A+ + S I + L+ A +E + I + ED Sbjct: 215 PQLTIRQMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDR 274 Query: 358 ALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQ 417 L ++I G A A Q + L +P + ER DL DL R+L+ L G+ Sbjct: 275 GWLSRIREAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGR 334 Query: 418 DWHYD---VPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLV 474 D +P ++ A + P++LL Q+ + G+ + EG +SHV I+AR +P + Sbjct: 335 KSEADGGTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIPVVQ 394 Query: 475 ALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHT 534 A A +P V++D D G+ + P A+A ++ + +A P+ T Sbjct: 395 APDALNRIEPL-DPVIVDGDHGQAFVRPAEDIQMAFAEAVALRARKEQMYEAIRAQPSVT 453 Query: 535 RDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDA 594 RDG+ I + N + GA+G+GL RTE F+ R T PD Q Y +LD Sbjct: 454 RDGVPISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRILDQ 513 Query: 595 MGDKSVIIRTIDVGGDKQLDYLPL-PAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSP 653 DK V+ RT+DVGGDK L Y+ E NP LG R IR+ P LL QQLRALL+ S Sbjct: 514 TDDKPVVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLRASA 573 Query: 654 LQRCRILLPMVTEVDELLYIRQRLDALCAEL-----ALTQRLELGVMIEVPAAALLAEQL 708 + ++ PM+ EV E R+ LD L R+ +G MIEVPA L Sbjct: 574 GRPLSVMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQLPAL 633 Query: 709 AEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVC 768 DFLS+G+NDL+QY A DR + + R D L PA++ L+ + V +C Sbjct: 634 LPRVDFLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPVSIC 693 Query: 769 GALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRF 814 G +A PL LIG+G LS+SPP VG +K +R LD A R++ Sbjct: 694 GEMAGRPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVAVLRQY 739 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: 1359 Number of extensions: 69 Number of successful extensions: 5 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: 838 Length of database: 766 Length adjustment: 41 Effective length of query: 797 Effective length of database: 725 Effective search space: 577825 Effective search space used: 577825 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