GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcA in Nocardioides daejeonensis MJ31

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate WP_110205669.1 DNK54_RS04295 arginine deiminase

Query= BRENDA::P13981
         (418 letters)



>NCBI__GCF_003194585.1:WP_110205669.1
          Length = 414

 Score =  528 bits (1359), Expect = e-154
 Identities = 248/407 (60%), Positives = 315/407 (77%), Gaps = 2/407 (0%)

Query: 9   GVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGID 68
           GVHSE G LRKV+VC+PGLAH RLTPSNCD+LLFDDV+WV  A+RDH +F+  M  RGI+
Sbjct: 7   GVHSEVGTLRKVLVCAPGLAHARLTPSNCDDLLFDDVMWVQNAQRDHAEFMELMSGRGIE 66

Query: 69  VLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVA 128
           VLE H LL+ET+Q PEA  W+LDRK+TA+ VGLGL  + R++LE+L   +LA YL+GG+A
Sbjct: 67  VLEFHQLLSETLQQPEARSWLLDRKVTANQVGLGLVDDTRAFLEALVAEELARYLVGGLA 126

Query: 129 ADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQE 188
             DLP     + L + R   G   +LLPPLPN  +TRDTTCWI  G+TLNP++WPAR  E
Sbjct: 127 VADLPDEHRTDYLALARGSRGVHEYLLPPLPNMLYTRDTTCWIGDGMTLNPLHWPARHDE 186

Query: 189 TLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQA 248
           TLL  A+Y FHP FA+A   +W+GDP+   G +TLEGGDVMP+GNGVVL+GM ER+SRQA
Sbjct: 187 TLLYKALYSFHPAFADAGIPVWWGDPEVSWGQATLEGGDVMPLGNGVVLVGMSERTSRQA 246

Query: 249 IGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRP 308
           I Q+A  LF  GAAE+V+VAG+PK R+AMHLDTV +F DRD+VT + +VV  + PF+LRP
Sbjct: 247 ITQLAARLFEGGAAEQVVVAGMPKMRSAMHLDTVLTFADRDVVTAYRDVVDHLAPFTLRP 306

Query: 309 DPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGV 368
                 G+++  E +   +VVA++LG+  +RV+ETGG+ +A+ER+QWD GNNVV LEPGV
Sbjct: 307 GVGG--GVHVTAERRHLTDVVAKALGIDGIRVIETGGDVYASERQQWDSGNNVVALEPGV 364

Query: 369 VVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDP 415
           VVGYDRNT+TN LL  AG+EV+TI  +ELGRGRGGGHCMTCP++RDP
Sbjct: 365 VVGYDRNTHTNALLEAAGIEVLTIVGAELGRGRGGGHCMTCPLLRDP 411


Lambda     K      H
   0.319    0.137    0.414 

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: 592
Number of extensions: 22
Number of successful extensions: 2
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: 418
Length of database: 414
Length adjustment: 31
Effective length of query: 387
Effective length of database: 383
Effective search space:   148221
Effective search space used:   148221
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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