Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate N515DRAFT_3957 N515DRAFT_3957 phosphotransferase system, enzyme I, PtsI
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >FitnessBrowser__Dyella79:N515DRAFT_3957 Length = 576 Score = 291 bits (745), Expect = 7e-83 Identities = 186/526 (35%), Positives = 269/526 (51%), Gaps = 11/526 (2%) Query: 304 IGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAAD 363 +G ++ + ++L AL R E+ R+ AH LL+D LL D Sbjct: 34 LGEDEVDVELEKLHRALDTARQELRELRGKLHGALAREVNEFIDAHSLLLDDQELLRGLD 93 Query: 364 LFIEQGSAAPHA-WSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLG----EAW 418 + G P A + D V + + L R D+ + RV+ L E Sbjct: 94 DLVRIGHYRPGAALKKQRDRLAAVFEAMDDPYLRSRKEDVDQVINRVISALQRQTSREER 153 Query: 419 QFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDE 478 + G I+ A + P+D+ L+ G+ GV G SH AILAR LP LV + D Sbjct: 154 KLAARVGEILIADTIAPADMAHLAGNGLLGVVASSGSPYSHSAILARSLDLPMLVGVRDA 213 Query: 479 LLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVE 538 L ++LDA+ G + PT + LA+ R Q + SLA+ P RT DG + Sbjct: 214 LATIHDDDLILLDAERGEAVVHPTAQDLARYRAWQREAQQEGRRLASLANAPTRTRDGTD 273 Query: 539 VEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKP 598 + + AN ++ + + A GADGVGL RTEFLF+ P E+EQ AY+ ++ MG P Sbjct: 274 IRLLANAETTTDIAMARARGADGVGLYRTEFLFLRHKGLPSEDEQFIAYRDLVLGMGGLP 333 Query: 599 VIIRTIDVGGDK-QLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCR 657 V IRT+D+G DK L L E NP LG+RG+RL+ P + Q+RA+L+ R Sbjct: 334 VTIRTLDLGADKADAAGLALRGEENPALGVRGVRLSLRYPAVFTTQIRAILRAACYGPVR 393 Query: 658 ILLPMVTEVDELLHIR-----KRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHAD 712 +L+PM+T+ DEL+ +R R D + L E+ QLG M+EVPAAA+ L EHAD Sbjct: 394 VLVPMITQPDELIAVRTLFKLARQDLKRENVDLPEKLQLGAMIEVPAAAINVRSLLEHAD 453 Query: 713 FLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALAS 772 FL+IGTNDL+QY LA DR + L + L PALLRLI+ + G+ V +CG + Sbjct: 454 FLAIGTNDLAQYVLASDRGNDALDNIYNPLQPALLRLISYVITSGRRAGKPVSLCGEIGG 513 Query: 773 DPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELL 818 D T +L+ LG+ E S+ Q+ ++DR+ L+ RL+ +L Sbjct: 514 DTKFTALLLALGLCEFSMHSSQLLHVRDRIASLNHKGLRRLAPAIL 559 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: 1004 Number of extensions: 44 Number of successful extensions: 4 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: 576 Length adjustment: 39 Effective length of query: 798 Effective length of database: 537 Effective search space: 428526 Effective search space used: 428526 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 Apr 09 2024. 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