Alignments for a candidate for rocF in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Dyella japonica UNC79MFTsu3.2

Align Arginase (EC 3.5.3.1) (characterized)
to candidate N515DRAFT_0348 N515DRAFT_0348 arginase

Query= reanno::Dyella79:N515DRAFT_0348
         (304 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0348
          Length = 304

 Score =  613 bits (1581), Expect = e-180
 Identities = 304/304 (100%), Positives = 304/304 (100%)

Query: 1   MGNQAVSLIGAPTDIGAGHRGASMGPEALRVANLQARLKARGIDVVDRGNLQGPLNPWEP 60
           MGNQAVSLIGAPTDIGAGHRGASMGPEALRVANLQARLKARGIDVVDRGNLQGPLNPWEP
Sbjct: 1   MGNQAVSLIGAPTDIGAGHRGASMGPEALRVANLQARLKARGIDVVDRGNLQGPLNPWEP 60

Query: 61  PREGYRHLSAVVDWNRAVYEAIYGELSLGRLPVMLGGDHCLAIGSITAVARHCREHHKKL 120
           PREGYRHLSAVVDWNRAVYEAIYGELSLGRLPVMLGGDHCLAIGSITAVARHCREHHKKL
Sbjct: 61  PREGYRHLSAVVDWNRAVYEAIYGELSLGRLPVMLGGDHCLAIGSITAVARHCREHHKKL 120

Query: 121 RVLWLDAHADFNTAQITPSGNIHGMPVACLCGMGPEELTTLGGSKPATAPDVFRQIGIRS 180
           RVLWLDAHADFNTAQITPSGNIHGMPVACLCGMGPEELTTLGGSKPATAPDVFRQIGIRS
Sbjct: 121 RVLWLDAHADFNTAQITPSGNIHGMPVACLCGMGPEELTTLGGSKPATAPDVFRQIGIRS 180

Query: 181 VDEGEKRLVREARVSIFDMRQIDESGMKRVMEEALEGVDADTHLHVSFDVDFLDPAIAPG 240
           VDEGEKRLVREARVSIFDMRQIDESGMKRVMEEALEGVDADTHLHVSFDVDFLDPAIAPG
Sbjct: 181 VDEGEKRLVREARVSIFDMRQIDESGMKRVMEEALEGVDADTHLHVSFDVDFLDPAIAPG 240

Query: 241 VGTTVRGGPNYREAQLCMEMIADTGRLASLDIVELNPAFDKRNQTAKLAVDLVESLFGKS 300
           VGTTVRGGPNYREAQLCMEMIADTGRLASLDIVELNPAFDKRNQTAKLAVDLVESLFGKS
Sbjct: 241 VGTTVRGGPNYREAQLCMEMIADTGRLASLDIVELNPAFDKRNQTAKLAVDLVESLFGKS 300

Query: 301 TLIR 304
           TLIR
Sbjct: 301 TLIR 304


Lambda     K      H
   0.320    0.137    0.412 

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: 520
Number of extensions: 19
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: 304
Length of database: 304
Length adjustment: 27
Effective length of query: 277
Effective length of database: 277
Effective search space:    76729
Effective search space used:    76729
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate N515DRAFT_0348 N515DRAFT_0348 (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.29428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.6e-94  301.9   0.0      3e-94  301.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348  N515DRAFT_0348 arginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0348  N515DRAFT_0348 arginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.7   0.0     3e-94     3e-94       1     299 [.       7     301 ..       7     302 .. 0.95

  Alignments for each domain:
  == domain 1  score: 301.7 bits;  conditional E-value: 3e-94
                                    TIGR01229   1 sivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaersvl 66 
                                                  s++g+p + G+g+rG  +Gp+alr a+l+++lk  + +v d g+++    + e +re+ +++ +v+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348   7 SLIGAPTDIGAGHRGASMGPEALRVANLQARLKARGIDVVDRGNLQGPLNPWEPPREGYRHLSAVV 72 
                                                  589*******************************************666777888*********** PP

                                    TIGR01229  67 aakeklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDintletst 130
                                                   ++++++e+++ +   +r+p++LggdH +aiG++++va++ +++  kl vlwlDAHaD+nt++ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348  73 DWNRAVYEAIYGELSLGRLPVMLGGDHCLAIGSITAVARHCREHhkKLRVLWLDAHADFNTAQITP 138
                                                  ****************************************999777******************** PP

                                    TIGR01229 131 SgnlHGmPlafllgrlkkevedleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmk 196
                                                  Sgn+HGmP+a l g   +e ++l   +  k+    p     iG+R+vdegE+++++e  + +f+m+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348 139 SGNIHGMPVACLCGMGPEELTTL---GGSKP-ATAPDVFRQIGIRSVDEGEKRLVREARVSIFDMR 200
                                                  **************444444444...45888.589******************************* PP

                                    TIGR01229 197 eidklGiakvvektleslkaedpihlSlDvDglDpklapatGtpvrgGltfrEgklilelllesgl 262
                                                  +id+ G+++v+e++le + a++ +h+S+DvD+lDp +ap++Gt+vrgG  +rE++l +e+++++g+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348 201 QIDESGMKRVMEEALEGVDADTHLHVSFDVDFLDPAIAPGVGTTVRGGPNYREAQLCMEMIADTGR 266
                                                  ****************************************************************** PP

                                    TIGR01229 263 ltaldlvEvNPtldikeksetikaavelvesllgetl 299
                                                  l +ld+vE+NP  d  ++++t+k av+lvesl+g++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0348 267 LASLDIVELNPAFD--KRNQTAKLAVDLVESLFGKST 301
                                                  **************..99****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (304 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.83
//
[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