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_076582194.1 BB347_RS06745 arginase

Query= SwissProt::P39138
         (296 letters)



>NCBI__GCF_001971705.1:WP_076582194.1
          Length = 306

 Score =  288 bits (737), Expect = 1e-82
 Identities = 153/308 (49%), Positives = 206/308 (66%), Gaps = 14/308 (4%)

Query: 1   MDKTISVIGMPMDLGQARRGVDMGPSAIRYAHLIERLSDMGYTVEDLGDIPINREKIKN- 59
           M +T+ ++G PMD G  RRGVDMGPSAIRYA L +RL D G T  D GD+ I R + ++ 
Sbjct: 1   MSETVRILGAPMDYGADRRGVDMGPSAIRYAGLADRLEDAGVTTIDDGDLSIPRAEERDP 60

Query: 60  ------DEELKNLNSVLAGNEKLAQKVNKVIEEKKFPLVLGGDHSIAIGTLAGTAKHYDN 113
                 D   K L  V     +L ++V   +E  +FPLVLGGDHS+AIG++ G+A+  D 
Sbjct: 61  DAEQPADGHAKFLREVEDVCTRLGERVESALENGEFPLVLGGDHSVAIGSMRGSARDAD- 119

Query: 114 LGVIWYDAHGDLNTLETSPSGNIHGMPLAVSLGIGHESLVNLEGYAPKIKPENVVIIGAR 173
           LG IW+DAH DLNT  TSPSGN+HGMPLA +LG G    V+   +AP+++ E++V +G R
Sbjct: 120 LGAIWFDAHADLNTPATSPSGNVHGMPLAATLGRGAFGDVDW-AHAPRVREESIVYVGLR 178

Query: 174 SLDEGERKYIKESGMKVYTMHEIDRLGMTKVIEETLDY-LSACDGVHLSLDLDGLDPNDA 232
           S+D+ ER+ ++ES M  +TM +ID  GMT V+E+ LD   S  DGVH+SLDLD LDP  A
Sbjct: 179 SIDDRERELVRESEMTAFTMADIDEYGMTAVVEDALDVATSGTDGVHVSLDLDWLDPKTA 238

Query: 233 PGVGTPVVGGISYRESHLAMEMLYD----AGIITSAEFVEVNPILDHKNKTGKTAVELVE 288
           PGVGTPV GG++YRE+H A+E +       G++ S + VEVNPILD +N+T + A EL  
Sbjct: 239 PGVGTPVRGGVTYREAHAALETVATRHGREGVVRSMDVVEVNPILDERNETARLAAELTA 298

Query: 289 SLLGKKLL 296
           S  G ++L
Sbjct: 299 SAFGNRIL 306


Lambda     K      H
   0.314    0.137    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: 302
Number of extensions: 14
Number of successful extensions: 6
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: 296
Length of database: 306
Length adjustment: 27
Effective length of query: 269
Effective length of database: 279
Effective search space:    75051
Effective search space used:    75051
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: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_076582194.1 BB347_RS06745 (arginase)
to HMM TIGR01229 (rocF: arginase (EC 3.5.3.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01229.hmm
# target sequence database:        /tmp/gapView.3448788.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01229  [M=300]
Accession:   TIGR01229
Description: rocF_arginase: arginase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.2e-93  297.0   0.0    9.2e-93  296.8   0.0    1.0  1  NCBI__GCF_001971705.1:WP_076582194.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001971705.1:WP_076582194.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.8   0.0   9.2e-93   9.2e-93       2     298 ..       7     304 ..       6     306 .] 0.93

  Alignments for each domain:
  == domain 1  score: 296.8 bits;  conditional E-value: 9.2e-93
                             TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesd.......reavkaersvla 67 
                                           i+g+p++ G+ +rGvd+Gp+a+r+agl+++l+d + +  d+g+++ + + +e d       +   k++r v  
  NCBI__GCF_001971705.1:WP_076582194.1   7 ILGAPMDYGADRRGVDMGPSAIRYAGLADRLEDAGVTTIDDGDLS-IPRAEERDpdaeqpaDGHAKFLREVED 78 
                                           89******************************************9.5555555557778887889******** PP

                             TIGR01229  68 akeklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdkklgvlwlDAHaDintletstSgnlHGmPla 140
                                           +  +l e v+   e+++fplvLggdHs+aiG++ g a+ a d  lg +w+DAHaD+nt+ ts+Sgn+HGmPla
  NCBI__GCF_001971705.1:WP_076582194.1  79 VCTRLGERVESALENGEFPLVLGGDHSVAIGSMRGSARDA-D--LGAIWFDAHADLNTPATSPSGNVHGMPLA 148
                                           ***********************************99764.4..8**************************** PP

                             TIGR01229 141 fllgrlkkevedleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGiakvvektles 213
                                             lgr  ++     ++++ +++ +  +++vy+GlR++d+ Er++++e+++++f+m +id++G+++vve +l+ 
  NCBI__GCF_001971705.1:WP_076582194.1 149 ATLGRGAFG-----DVDWAHAPRVREESIVYVGLRSIDDRERELVRESEMTAFTMADIDEYGMTAVVEDALDV 216
                                           ****54444.....467888889************************************************98 PP

                             TIGR01229 214 lkaed.pihlSlDvDglDpklapatGtpvrgGltfrEgklilellle....sglltaldlvEvNPtldikeks 281
                                            ++ +  +h+SlD+D lDpk+ap++GtpvrgG+t+rE++ +le+++     +g + ++d+vEvNP+ld  e++
  NCBI__GCF_001971705.1:WP_076582194.1 217 ATSGTdGVHVSLDLDWLDPKTAPGVGTPVRGGVTYREAHAALETVATrhgrEGVVRSMDVVEVNPILD--ERN 287
                                           765444***************************************98878899***************..*** PP

                             TIGR01229 282 etikaavelvesllget 298
                                           et++ a el++s++g+ 
  NCBI__GCF_001971705.1:WP_076582194.1 288 ETARLAAELTASAFGNR 304
                                           **************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (306 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.11
//
[ok]

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