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

GapMind for catabolism of small carbon sources

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

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Ac3H11_3541 UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)

Query= BRENDA::Q8PK83
         (297 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3541
          Length = 295

 Score =  306 bits (783), Expect = 5e-88
 Identities = 161/285 (56%), Positives = 198/285 (69%), Gaps = 2/285 (0%)

Query: 5   IRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYKHS 64
           +RKAVFPVAGLGTRFLPATK  PKEMLP++DKPLIQYAV+EA  AG   +IFVT R K +
Sbjct: 7   VRKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAYAAGIRHMIFVTGRSKRA 66

Query: 65  IADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAVVG 124
           I D+FD AYELE +LE A K E L LVR   PD +   FV Q  +LGLGHAVLCA+ +VG
Sbjct: 67  IEDHFDTAYELEAELEAANKKELLALVRSIQPDDMDCAFVRQPRSLGLGHAVLCAEPLVG 126

Query: 125 NEPFAVLLPDDLMWN--RGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFD 182
            EPFAVLL DDLM     G   L QMA+     G SVIAV++VP D+   YGIV+ +   
Sbjct: 127 KEPFAVLLADDLMVGPPGGQPVLAQMASAFRQQGRSVIAVQEVPEDQVHKYGIVAGEPAG 186

Query: 183 GRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLK 242
           G   RI  IVEKPK +VAPS + V GRY+L+P +FD +     G GGEIQLTD IA L++
Sbjct: 187 GPLIRIERIVEKPKADVAPSRMGVAGRYILTPGVFDEIRNQPRGVGGEIQLTDGIARLMQ 246

Query: 243 EEQVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHGGPAKEILR 287
            E V AF+++G+R+DCG+  G +EATV  AL+H + G   +E L+
Sbjct: 247 HEAVYAFQYQGKRYDCGSKEGFLEATVELALQHPQVGAHFREYLK 291


Lambda     K      H
   0.319    0.137    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: 277
Number of extensions: 8
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: 297
Length of database: 295
Length adjustment: 26
Effective length of query: 271
Effective length of database: 269
Effective search space:    72899
Effective search space used:    72899
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 Ac3H11_3541 (UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))
to HMM TIGR01099 (galU: UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))

# 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/TIGR01099.hmm
# target sequence database:        /tmp/gapView.5316.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01099  [M=261]
Accession:   TIGR01099
Description: galU: UTP--glucose-1-phosphate uridylyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.2e-113  362.5   0.0   8.2e-113  362.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541  UTP--glucose-1-phosphate uridyly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541  UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.3   0.0  8.2e-113  8.2e-113       1     261 []       7     271 ..       7     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.3 bits;  conditional E-value: 8.2e-113
                                        TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraie 62 
                                                      +rkav+P+aGlGtr+LPatka Pkemlp+vdkPliqy+veea +aGi ++++vtgrskraie
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541   7 VRKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAYAAGIRHMIFVTGRSKRAIE 68 
                                                      79************************************************************ PP

                                        TIGR01099  63 dhfDtsyeleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepf 123
                                                      dhfDt+yelea+le +nk+ell  vr+i++  +++ +vrq +  GLGhavl+ae+lvg+epf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541  69 DHFDTAYELEAELEAANKKELLALVRSIQPDdMDCAFVRQPRSLGLGHAVLCAEPLVGKEPF 130
                                                      *****************************988****************************** PP

                                        TIGR01099 124 avllgDdlvseeee...alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyev 182
                                                      avll+Ddl++       +l+q+ +++++ g s+iav+evp+++v+kYG+++ge     l+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541 131 AVLLADDLMVGPPGgqpVLAQMASAFRQQGRSVIAVQEVPEDQVHKYGIVAGEPAGGPLIRI 192
                                                      *********98654555********************************************* PP

                                        TIGR01099 183 kdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkggeiqltDalrlllekeevlavk 244
                                                      + +vekPk++ aps + + GrY+ltp +f+ ++++++G+ggeiqltD+++ l+++e+v+a++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541 193 ERIVEKPKADVAPSRMGVAGRYILTPGVFDEIRNQPRGVGGEIQLTDGIARLMQHEAVYAFQ 254
                                                      ************************************************************** PP

                                        TIGR01099 245 lkgkryDvGdklgylka 261
                                                       +gkryD+G+k+g+l+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3541 255 YQGKRYDCGSKEGFLEA 271
                                                      ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (295 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: 00:00:00.01
# Mc/sec: 7.57
//
[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