Align N-acetylglucosamine 6-phosphate deacetylase (NagA;BSU35010) (EC 3.5.1.25) (characterized)
to candidate Echvi_4311 Echvi_4311 N-acetylglucosamine-6-phosphate deacetylase
Query= CAZy::CAB15506.1 (396 letters) >FitnessBrowser__Cola:Echvi_4311 Length = 386 Score = 129 bits (325), Expect = 1e-34 Identities = 98/325 (30%), Positives = 152/325 (46%), Gaps = 12/325 (3%) Query: 54 VLLPGMIDIHIHGGYGADTMDASFSTLDIMSS--RLPEEGTTSFLATTITQEHGNISQAL 111 ++ PG++D+ ++G G D + + +++S RL E G T+F T IT +S A+ Sbjct: 41 MIAPGLVDLQVNGFQGVDFNEPGLTVDEVVSCTRRLWENGVTTFFPTLITASEAALSDAI 100 Query: 112 VNAREWKAAEESSLLGAELLGIHLEGPFVSPKRA--GAQPKEWIRPSDVELFKKWQQEAG 169 ++ A + ++ + GIHLEGPF+S GA P ++++ + L + Q+ A Sbjct: 101 ---KKIVQACQDPVIARTIAGIHLEGPFISKDAGPRGAHPLKYVQAPNWGLVSRLQKVAK 157 Query: 170 GLIKIVTLAPEEDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMS 229 G IK+VTL+PE DQ E+I+ E I ++GHT A + L A + GA THL NA Sbjct: 158 GKIKLVTLSPEHDQTNEVIKKCVAEQIHVAIGHTAAKTDQLGKAVEVGADLSTHLGNAAH 217 Query: 230 PFHHREPGVIGTALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLK 289 R P I LA DG T +I+DG H P A F+ K L++DS + G Sbjct: 218 LSLPRHPNYIWDQLALDGLWTSMISDGFHL-PDAVMKVFMRVKPDKTFLVSDSTKFAGQP 276 Query: 290 DGVYE--FGGQSVTVRGRTALLSD--GTLAGSILKMNEGARHMREFTNCSWTDIANITSE 345 G Y+ GG G + D LAGS + ++ S ++ S Sbjct: 277 AGSYQSPIGGTVRLSPGGRLCMQDNPNLLAGSAASLKSCLEYLARAKLASLPQAIDMASI 336 Query: 346 NAAKQLGIFDRKGSVTVGKDADLVI 370 L + + G AD+V+ Sbjct: 337 RPLSYLAKGKKIKAFQKGSRADVVL 361 Lambda K H 0.316 0.132 0.377 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: 316 Number of extensions: 15 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: 396 Length of database: 386 Length adjustment: 31 Effective length of query: 365 Effective length of database: 355 Effective search space: 129575 Effective search space used: 129575 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 (21.6 bits) S2: 50 (23.9 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