Align Predicted dapE by GapMind curators (no experimental data)
to candidate WP_044138386.1 GQW_RS0102470 amidohydrolase
Query= predicted:L0FXC2 (397 letters) >NCBI__GCF_000220155.1:WP_044138386.1 Length = 404 Score = 436 bits (1122), Expect = e-127 Identities = 212/395 (53%), Positives = 283/395 (71%), Gaps = 2/395 (0%) Query: 2 LKDTIKKLAADQLNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKANTGL 61 LK I KL QL+ IA RRHIH +PELSF EH T +V LQ+ GI + A TG+ Sbjct: 4 LKQLINKLTKVQLDSIIADRRHIHQNPELSFNEHNTSDYVASRLQQAGIPFRRGVAGTGI 63 Query: 62 VALIEGKNPSKKVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASIL 121 +A ++GKNP + IALRADMDALPI E+ ++P+ S +G+MHACGHD HT+ L+G A+IL Sbjct: 64 IATLQGKNPGR-TIALRADMDALPIQEETNLPFASVNKGIMHACGHDAHTAVLIGVANIL 122 Query: 122 HAVKDQFEGTVKLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFR 181 + ++DQ+ GT+ IFQPGEEK PGGASL++K+ AL+NP+P ++GQHV+P + AGKVGF+ Sbjct: 123 NQLRDQWNGTILFIFQPGEEKFPGGASLLLKEGALDNPKPDLVIGQHVLPEMAAGKVGFK 182 Query: 182 KGMYMASADELYLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSF 241 GMYMAS DE+YL V GKGGH A+P TL D +LIASHIIVALQQ++SR +P+VLSF Sbjct: 183 PGMYMASGDEVYLTVSGKGGHAALPHTLNDNILIASHIIVALQQIVSRMVPTTIPTVLSF 242 Query: 242 GRIEALGATNVIPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGY 301 GRIE LGATN+IP +V I GT RTLDE WR +++ +IAEG A MG +++ GY Sbjct: 243 GRIEGLGATNIIPEKVEIAGTLRTLDEEWRGLIKKRIKEIAEGTAAAMGAHCHVDIKDGY 302 Query: 302 PFLQNAPELTDRAYKAAQAYLGEENVEDLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKG 361 P + N P+ T +A A+ +LGE VE++ + M AEDF YYTQ+ FYR G+ +E+G Sbjct: 303 PVVYNNPDATKKAIAWAKNFLGENRVEEMGVRMTAEDFGYYTQQFPSVFYRFGVA-QEQG 361 Query: 362 ITSGVHTPTFDIDESALEVGAGLMAWIAINELMSE 396 T +HTP F+++E ALE ++AW+A+N L S+ Sbjct: 362 TTCALHTPHFNLNEKALETATSVLAWLAVNFLQSD 396 Lambda K H 0.317 0.134 0.387 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: 489 Number of extensions: 16 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: 397 Length of database: 404 Length adjustment: 31 Effective length of query: 366 Effective length of database: 373 Effective search space: 136518 Effective search space used: 136518 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 Jul 26 2024. The underlying query database was built on Jul 25 2024.
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