Alignments for a candidate for rocF in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Dinoroseobacter shibae DFL-12

Align arginase subunit (EC 3.5.3.1) (characterized)
to candidate 3608918 Dshi_2309 arginase (RefSeq)

Query= metacyc::MONOMER-11552
         (324 letters)



>FitnessBrowser__Dino:3608918
          Length = 308

 Score =  350 bits (897), Expect = e-101
 Identities = 179/302 (59%), Positives = 216/302 (71%), Gaps = 4/302 (1%)

Query: 21  CQILGAPVQSGASQPGCLMGPDAFRTAGLTQVLTELGWAVTDLGDAT-PTVEPELSHPNS 79
           C ++GA +  G  + GCLMGPDA+RTAGL   L +LGW   D G+   PT   +   P  
Sbjct: 6   CILIGAGMDCGKRRRGCLMGPDAYRTAGLIDTLGDLGWQTEDRGNLPGPTWVADT--PPG 63

Query: 80  AVKNLDALVGWTRSLSQKALEMARSCDLPVFLGGDHSMSAGTVSGVAQRTAELGKEQFVL 139
            +  L   + WTR LS+ A + A     P+FLGGDH++S GTV+GV+   A   +  FVL
Sbjct: 64  ELHALSETITWTRLLSEAA-QAAIGQGFPIFLGGDHALSLGTVAGVSAHAAGQDRPLFVL 122

Query: 140 WLDAHTDLHTLHTTASGNLHGTPVAYYTGQSGFEGLPPLAAPVNPRNVSMMGIRSVDPEE 199
           WLDAH D++T  TT SGNLHGTPVAY TGQ+GF+G P L APV P N+  +G+RSVD  E
Sbjct: 123 WLDAHPDINTPTTTLSGNLHGTPVAYITGQAGFDGFPTLTAPVPPENICFIGLRSVDASE 182

Query: 200 RRRVAEIGVQVADMRVLDEQGVVRPLEAFLDRVSKVSGRLHVSLDVDFLDPAIAPAVGTT 259
           R  +A+ G+   DMR +DE G+  PL AFL RV+   G LHVSLDVDFL+PAIAPAVGTT
Sbjct: 183 RNFIAQSGMTAIDMRQIDEHGIAAPLSAFLARVATAGGMLHVSLDVDFLEPAIAPAVGTT 242

Query: 260 VPGGATFREAHLIMEMLHDSGLVTSLDLAELNPFLDERGRTARLITDLASSLFGRRVFDR 319
           VPGGATFREAHL+MEMLHDSGLV+SLDL ELNPFLD+RGRTA L+ DL +SLFGRRVFDR
Sbjct: 243 VPGGATFREAHLVMEMLHDSGLVSSLDLVELNPFLDDRGRTASLMVDLTASLFGRRVFDR 302

Query: 320 VT 321
            T
Sbjct: 303 PT 304


Lambda     K      H
   0.318    0.134    0.393 

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: 344
Number of extensions: 15
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: 324
Length of database: 308
Length adjustment: 27
Effective length of query: 297
Effective length of database: 281
Effective search space:    83457
Effective search space used:    83457
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)

Align candidate 3608918 Dshi_2309 (arginase (RefSeq))
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.18627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.1e-91  293.2   0.0    1.3e-91  293.0   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608918  Dshi_2309 arginase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608918  Dshi_2309 arginase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.0   0.0   1.3e-91   1.3e-91       2     298 ..       8     298 ..       7     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: 293.0 bits;  conditional E-value: 1.3e-91
                         TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaersvlaakeklaekvkk 78 
                                       ++g++++ G+ +rG+ +Gp+a+r agl+++l+dl+ + ed g+++  + + +++  +++a+    ++++ l+e+++ 
  lcl|FitnessBrowser__Dino:3608918   8 LIGAGMDCGKRRRGCLMGPDAYRTAGLIDTLGDLGWQTEDRGNLPGPTWVADTPPGELHALSETITWTRLLSEAAQA 84 
                                       89*******************************************99****************************** PP

                         TIGR01229  79 vveekrfplvLggdHsiaiGtvsgvakka..kdkklgvlwlDAHaDintletstSgnlHGmPlafllgrlkkevedl 153
                                        + ++ fp++LggdH++ +Gtv+gv  +a  +d+ l+vlwlDAH Dint+ t+ SgnlHG+P+a+++g+++++   +
  lcl|FitnessBrowser__Dino:3608918  85 AIGQG-FPIFLGGDHALSLGTVAGVSAHAagQDRPLFVLWLDAHPDINTPTTTLSGNLHGTPVAYITGQAGFDG--F 158
                                       **999.*******************9887235779*********************************988888..7 PP

                         TIGR01229 154 eelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGiakvvektleslkaed.pihlSlDvDgl 229
                                       +   l+++  + p+++++iGlR+vd++Er+ + ++g+++ +m++id++Gia+ +  +l+++ +   ++h+SlDvD+l
  lcl|FitnessBrowser__Dino:3608918 159 PT--LTAP--VPPENICFIGLRSVDASERNFIAQSGMTAIDMRQIDEHGIAAPLSAFLARVATAGgMLHVSLDVDFL 231
                                       87..4445..99*************************************************99988*********** PP

                         TIGR01229 230 DpklapatGtpvrgGltfrEgklilelllesglltaldlvEvNPtldikeksetikaavelvesllget 298
                                       +p +apa+Gt+v+gG+tfrE++l++e+l++sgl+++ldlvE+NP+ld  ++++t++ +v+l++sl+g+ 
  lcl|FitnessBrowser__Dino:3608918 232 EPAIAPAVGTTVPGGATFREAHLVMEMLHDSGLVSSLDLVELNPFLD--DRGRTASLMVDLTASLFGRR 298
                                       ***********************************************..*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (308 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.48
//
[ok]

This GapMind analysis is from Sep 17 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources