GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Thermophagus xiamenensis HS1

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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