GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocF in Haloterrigena daqingensis JX313

Align arginase (EC 3.5.3.1) (characterized)
to candidate WP_076579068.1 BB347_RS01540 agmatinase

Query= metacyc::MONOMER-14987
         (338 letters)



>NCBI__GCF_001971705.1:WP_076579068.1
          Length = 302

 Score =  114 bits (286), Expect = 2e-30
 Identities = 88/273 (32%), Positives = 143/273 (52%), Gaps = 30/273 (10%)

Query: 63  LLGVPLGHNSSFLQGPAFAPPRIREAM--WCGSTNSTTEEGKELDDPRILTDVGDVPVQE 120
           ++G PL  +++F  G  F P RIR     +      T +   +L     +TD GDV   +
Sbjct: 41  VVGAPLDVSTTFQPGTRFGPRRIRTFAEPFDDYDRRTDQHFSQLG----VTDHGDVRAWD 96

Query: 121 LRDAGVDDDRLMSIISESVKLVMEENPLRPLVLGGDHSISYPVVRAVSEKLGGPIDILHL 180
                 D +  +  +  +++ V+ ++ + PL+LGG+H++S   VRAVS ++     ++ L
Sbjct: 97  ------DVEAYLEYLEGTLRDVVWDDAV-PLMLGGEHTVSLAGVRAVSPEV-----VVCL 144

Query: 181 DAHPDIYHAFEGNKYSHASSFARIMEGGYARRLLQVGIRSINKE--GREQGKRFGVEQYE 238
           DAH D+Y A++GN++SHA+   RI+E      ++ +G+R+ ++E  GR   +   V    
Sbjct: 145 DAHLDLYDAYDGNEHSHAAVMRRILEVESVEEVILLGVRTGSEEEWGRAAAEDVTVVPPV 204

Query: 239 MRTFSQDRQFLENLKLGEGVKGVYISVDVDCMDPAFAPGVSHIEPGGLSFRDVLNILHNL 298
                +    LEN       + VY+SVD+D  DPA+APG    EP GL  R++ +++  L
Sbjct: 205 DVADWEPGAELEN-------RDVYLSVDIDAADPAYAPGTGTTEPFGLEPREMRDVVRAL 257

Query: 299 QADVVGADVVEFNPQRDTVDGMTAMVAAKLVRE 331
                G DVVE N   D  DG  A +A KL+RE
Sbjct: 258 APHAGGFDVVEVN---DRDDGQAASLAGKLLRE 287


Lambda     K      H
   0.318    0.136    0.389 

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: 292
Number of extensions: 17
Number of successful extensions: 5
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: 338
Length of database: 302
Length adjustment: 28
Effective length of query: 310
Effective length of database: 274
Effective search space:    84940
Effective search space used:    84940
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 (21.7 bits)
S2: 48 (23.1 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