Alignments for a candidate for rocF in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Herbaspirillum seropedicae SmR1

Align Arginase (EC 3.5.3.1) (characterized)
to candidate HSERO_RS00305 HSERO_RS00305 arginase

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



>FitnessBrowser__HerbieS:HSERO_RS00305
          Length = 302

 Score =  411 bits (1056), Expect = e-119
 Identities = 206/300 (68%), Positives = 238/300 (79%), Gaps = 3/300 (1%)

Query: 65  LIGAPTDIGAGARGASMGPEALRVAGLQAALELHGLQVFDRGNLGGPSNPWLPPVNGYRH 124
           ++GAPTD+GA  RGASM P ALRVA LQ  L+ HGL V D G+L GP+NP  PPV G RH
Sbjct: 6   MMGAPTDVGASRRGASMAPAALRVAELQRGLQQHGLDVIDGGDLAGPANPQQPPVQGLRH 65

Query: 125 LPEVAQWNRLVYDAVYAELQLGHLPILLGGDHSLGLGSISAVARHCAESGKKLRVLWLDA 184
           L +V QWN+ V++AV   L  G LP+L+GGDH+L +GSI+AVA HC   GK+LRVLWLDA
Sbjct: 66  LEQVVQWNQTVHEAVAQCLADGELPLLMGGDHALAVGSIAAVAAHCRSQGKELRVLWLDA 125

Query: 185 HADFNTSELTPSGNVHGMPVACLCGFGPAELTQLAAMPGGGPALRPEQIRQIGIRSVDAG 244
           HAD NTS+ TP+GN+HGMPVACL G GPA LT   A+ G  PAL+P+QI Q+GIRSVD  
Sbjct: 126 HADANTSQSTPTGNIHGMPVACLLGVGPAALT---AIGGQTPALQPQQICQVGIRSVDRE 182

Query: 245 EKRFVHEQGLEVFDMRAIDEVGMRQVMERALAGMDAHTHLHVSFDVDFLDPDIAPGVGTT 304
           EKR + E G+ VFDMR IDE GMRQ ME ALAG+   THLHVSFDVDFLD  +APGVGT 
Sbjct: 183 EKRHLRELGVRVFDMRHIDEYGMRQTMEEALAGVGPQTHLHVSFDVDFLDAALAPGVGTA 242

Query: 305 VPGGPTYREAQLCMEMIADSGRLASLDIVELNPALDVRNKTAVLAVDLVESLFGKSTLMR 364
           VPGGPTYREAQLCMEMIAD+G LASLD++ELNPA DVRN+TA L VDLVESLFGKSTL+R
Sbjct: 243 VPGGPTYREAQLCMEMIADTGALASLDVMELNPACDVRNQTAELVVDLVESLFGKSTLIR 302


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: 417
Number of extensions: 16
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: 368
Length of database: 302
Length adjustment: 28
Effective length of query: 340
Effective length of database: 274
Effective search space:    93160
Effective search space used:    93160
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 HSERO_RS00305 HSERO_RS00305 (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.6563.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    8.8e-91  290.3   0.0      1e-90  290.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00305  HSERO_RS00305 arginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00305  HSERO_RS00305 arginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.1   0.0     1e-90     1e-90       2     299 ..       6     299 ..       5     300 .. 0.95

  Alignments for each domain:
  == domain 1  score: 290.1 bits;  conditional E-value: 1e-90
                                  TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaersvlaak 69 
                                                ++g+p + G+++rG  + p alr a l+  l++ + +v d g++a    +++ + ++++++++v++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS00305   6 MMGAPTDVGASRRGASMAPAALRVAELQRGLQQHGLDVIDGGDLAGPANPQQPPVQGLRHLEQVVQWN 73 
                                                5799*****************************************888899999************** PP

                                  TIGR01229  70 eklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDintletstSgnlH 135
                                                +++ e+v++  +++++pl++ggdH++a+G++++va + + +  +l vlwlDAHaD nt ++++ gn+H
  lcl|FitnessBrowser__HerbieS:HSERO_RS00305  74 QTVHEAVAQCLADGELPLLMGGDHALAVGSIAAVAAHCRSQgkELRVLWLDAHADANTSQSTPTGNIH 141
                                                ************************************99876669************************ PP

                                  TIGR01229 136 GmPlafllgrlkkev.edleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklG 202
                                                GmP+a llg ++    + + +    ++  ++p++++ +G+R+vd+ E++ l+elg++vf+m++id++G
  lcl|FitnessBrowser__HerbieS:HSERO_RS00305 142 GMPVACLLG-VGPAAlTAIGG---QTP-ALQPQQICQVGIRSVDREEKRHLRELGVRVFDMRHIDEYG 204
                                                *********.66665244444...777.6*************************************** PP

                                  TIGR01229 203 iakvvektleslkaedpihlSlDvDglDpklapatGtpvrgGltfrEgklilelllesglltaldlvE 270
                                                + + +e++l+ + +++ +h+S+DvD+lD  lap++Gt v+gG t+rE++l +e+++++g l +ld++E
  lcl|FitnessBrowser__HerbieS:HSERO_RS00305 205 MRQTMEEALAGVGPQTHLHVSFDVDFLDAALAPGVGTAVPGGPTYREAQLCMEMIADTGALASLDVME 272
                                                ******************************************************************** PP

                                  TIGR01229 271 vNPtldikeksetikaavelvesllgetl 299
                                                +NP  d   +++t++ +v+lvesl+g++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS00305 273 LNPACD--VRNQTAELVVDLVESLFGKST 299
                                                ******..899***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (302 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: 7.22
//
[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