Alignments for a candidate for rocF in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Acidovorax sp. GW101-3H11

Align Arginase (EC 3.5.3.1) (characterized)
to candidate Ac3H11_701 Arginase (EC 3.5.3.1)

Query= reanno::acidovorax_3H11:Ac3H11_701
         (368 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_701
          Length = 368

 Score =  750 bits (1936), Expect = 0.0
 Identities = 368/368 (100%), Positives = 368/368 (100%)

Query: 1   VDTRTVHKGHGGLISPRTVHWHPKPRECPGATARAAAWPLPLSTPAQKALTMPPNTLRSA 60
           VDTRTVHKGHGGLISPRTVHWHPKPRECPGATARAAAWPLPLSTPAQKALTMPPNTLRSA
Sbjct: 1   VDTRTVHKGHGGLISPRTVHWHPKPRECPGATARAAAWPLPLSTPAQKALTMPPNTLRSA 60

Query: 61  QPTSLIGAPTDIGAGARGASMGPEALRVAGLQAALELHGLQVFDRGNLGGPSNPWLPPVN 120
           QPTSLIGAPTDIGAGARGASMGPEALRVAGLQAALELHGLQVFDRGNLGGPSNPWLPPVN
Sbjct: 61  QPTSLIGAPTDIGAGARGASMGPEALRVAGLQAALELHGLQVFDRGNLGGPSNPWLPPVN 120

Query: 121 GYRHLPEVAQWNRLVYDAVYAELQLGHLPILLGGDHSLGLGSISAVARHCAESGKKLRVL 180
           GYRHLPEVAQWNRLVYDAVYAELQLGHLPILLGGDHSLGLGSISAVARHCAESGKKLRVL
Sbjct: 121 GYRHLPEVAQWNRLVYDAVYAELQLGHLPILLGGDHSLGLGSISAVARHCAESGKKLRVL 180

Query: 181 WLDAHADFNTSELTPSGNVHGMPVACLCGFGPAELTQLAAMPGGGPALRPEQIRQIGIRS 240
           WLDAHADFNTSELTPSGNVHGMPVACLCGFGPAELTQLAAMPGGGPALRPEQIRQIGIRS
Sbjct: 181 WLDAHADFNTSELTPSGNVHGMPVACLCGFGPAELTQLAAMPGGGPALRPEQIRQIGIRS 240

Query: 241 VDAGEKRFVHEQGLEVFDMRAIDEVGMRQVMERALAGMDAHTHLHVSFDVDFLDPDIAPG 300
           VDAGEKRFVHEQGLEVFDMRAIDEVGMRQVMERALAGMDAHTHLHVSFDVDFLDPDIAPG
Sbjct: 241 VDAGEKRFVHEQGLEVFDMRAIDEVGMRQVMERALAGMDAHTHLHVSFDVDFLDPDIAPG 300

Query: 301 VGTTVPGGPTYREAQLCMEMIADSGRLASLDIVELNPALDVRNKTAVLAVDLVESLFGKS 360
           VGTTVPGGPTYREAQLCMEMIADSGRLASLDIVELNPALDVRNKTAVLAVDLVESLFGKS
Sbjct: 301 VGTTVPGGPTYREAQLCMEMIADSGRLASLDIVELNPALDVRNKTAVLAVDLVESLFGKS 360

Query: 361 TLMRTRPV 368
           TLMRTRPV
Sbjct: 361 TLMRTRPV 368


Lambda     K      H
   0.319    0.137    0.422 

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: 645
Number of extensions: 15
Number of successful extensions: 1
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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: 49 (23.5 bits)

Align candidate Ac3H11_701 (Arginase (EC 3.5.3.1))
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.10929.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    5.7e-91  290.9   0.0    6.7e-91  290.7   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701  Arginase (EC 3.5.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701  Arginase (EC 3.5.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.7   0.0   6.7e-91   6.7e-91       1     299 [.      64     361 ..      64     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 290.7 bits;  conditional E-value: 6.7e-91
                                       TIGR01229   1 sivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaer 63 
                                                     s++g+p + G+g rG  +Gp+alr agl+++l+  + +v d g++   + +   + ++ ++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701  64 SLIGAPTDIGAGARGASMGPEALRVAGLQAALELHGLQVFDRGNLGGPSNPWLPPVNGYRHLP 126
                                                     589*******************************************888888888******** PP

                                       TIGR01229  64 svlaakeklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDin 124
                                                      v ++++ ++++v+ + + +++p++LggdHs+ +G++s+va++ ++   kl vlwlDAHaD+n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701 127 EVAQWNRLVYDAVYAELQLGHLPILLGGDHSLGLGSISAVARHCAESgkKLRVLWLDAHADFN 189
                                                     ********************************************99766************** PP

                                       TIGR01229 125 tletstSgnlHGmPlafllgrlkkevedleelkllkgk..eispkklvyiGlRdvdegErkil 185
                                                     t e ++Sgn+HGmP+a l g    e ++l     ++g+   + p+++  iG+R+vd+gE++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701 190 TSELTPSGNVHGMPVACLCGFGPAELTQLAA---MPGGgpALRPEQIRQIGIRSVDAGEKRFV 249
                                                     ********************55555555555...5544469********************** PP

                                       TIGR01229 186 kelgikvfsmkeidklGiakvvektleslkaedpihlSlDvDglDpklapatGtpvrgGltfr 248
                                                     +e+g++vf+m++id+ G+ +v+e++l+ + a++ +h+S+DvD+lDp +ap++Gt+v+gG t+r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701 250 HEQGLEVFDMRAIDEVGMRQVMERALAGMDAHTHLHVSFDVDFLDPDIAPGVGTTVPGGPTYR 312
                                                     *************************************************************** PP

                                       TIGR01229 249 EgklilelllesglltaldlvEvNPtldikeksetikaavelvesllgetl 299
                                                     E++l +e++++sg+l +ld+vE+NP ld   +++t+  av+lvesl+g++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_701 313 EAQLCMEMIADSGRLASLDIVELNPALD--VRNKTAVLAVDLVESLFGKST 361
                                                     ****************************..899***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (368 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: 11.71
//
[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