Alignments for a candidate for galU in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Herbaspirillum seropedicae SmR1

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate HSERO_RS13375 HSERO_RS13375 UTP--glucose-1-phosphate uridylyltransferase

Query= BRENDA::Q8PK83
         (297 letters)



>FitnessBrowser__HerbieS:HSERO_RS13375
          Length = 335

 Score =  325 bits (834), Expect = 7e-94
 Identities = 167/296 (56%), Positives = 219/296 (73%), Gaps = 2/296 (0%)

Query: 3   QRIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYK 62
           ++I KAVFPVAGLG+RFLPATK  PKEMLPI+DKPLIQYAV+EA++AG   +IF+T R K
Sbjct: 2   KKITKAVFPVAGLGSRFLPATKAQPKEMLPIVDKPLIQYAVEEAVEAGITEMIFITGRNK 61

Query: 63  HSIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAV 122
            +I D+FDKAYELE +LE AGK++ LE +RH +P  +  ++V QAE LGLGHAVL AK +
Sbjct: 62  RAIEDHFDKAYELESELEAAGKVKLLETIRHVVPKHINCVYVRQAEPLGLGHAVLLAKPL 121

Query: 123 VGNEPFAVLLPDDLM-WNRGDA-ALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDA 180
           VG+EPFAVLL DD M  + G    + QM  + E  G S++AV+DVP  +T  YGIVS  A
Sbjct: 122 VGDEPFAVLLADDFMDVDAGQKNVMAQMTAMFEREGKSLLAVQDVPRPETRQYGIVSGSA 181

Query: 181 FDGRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAEL 240
           +  R   ++ IVEKP PE APS LAVVGRYVL+P IF+ LE  G GAGGEIQLTDAI+ L
Sbjct: 182 YADRLELMSGIVEKPAPEEAPSTLAVVGRYVLTPAIFERLENIGTGAGGEIQLTDAISAL 241

Query: 241 LKEEQVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHGGPAKEILREALAQADVR 296
           L++EQ+ A+R+EG+RFDCG+ +G ++A V    +H++ G    + L++  AQ D++
Sbjct: 242 LQQEQILAYRYEGQRFDCGSKLGYLKAAVAMGFKHKEVGSGFAQFLQDFAAQHDLQ 297


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: 310
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: 335
Length adjustment: 27
Effective length of query: 270
Effective length of database: 308
Effective search space:    83160
Effective search space used:    83160
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 HSERO_RS13375 HSERO_RS13375 (UTP--glucose-1-phosphate uridylyltransferase)
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.9739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.7e-115  370.4   0.0   3.2e-115  370.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS13375  HSERO_RS13375 UTP--glucose-1-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS13375  HSERO_RS13375 UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.2   0.0  3.2e-115  3.2e-115       1     261 []       4     268 ..       4     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.2 bits;  conditional E-value: 3.2e-115
                                  TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDts 68 
                                                i kav+P+aGlG r+LPatka+PkemlpivdkPliqy+veeaveaGi+e++++tgr+kraiedhfD++
  lcl|FitnessBrowser__HerbieS:HSERO_RS13375   4 ITKAVFPVAGLGSRFLPATKAQPKEMLPIVDKPLIQYAVEEAVEAGITEMIFITGRNKRAIEDHFDKA 71 
                                                68****************************************************************** PP

                                  TIGR01099  69 yeleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvsee 135
                                                yele++le ++k +ll+++r+++++ ++++yvrq e  GLGhavlla++lvgdepfavll+Dd ++ +
  lcl|FitnessBrowser__HerbieS:HSERO_RS13375  72 YELESELEAAGKVKLLETIRHVVPKhINCVYVRQAEPLGLGHAVLLAKPLVGDEPFAVLLADDFMDVD 139
                                                ***********************998*************************************99765 PP

                                  TIGR01099 136 ee...alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlai 200
                                                     +++q+++++e+ g+s +av++vp+ e+++YG+++g+   ++l  ++ +vekP peeaps la+
  lcl|FitnessBrowser__HerbieS:HSERO_RS13375 140 AGqknVMAQMTAMFEREGKSLLAVQDVPRPETRQYGIVSGSAYADRLELMSGIVEKPAPEEAPSTLAV 207
                                                444459************************************************************** PP

                                  TIGR01099 201 vGrYvltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                                vGrYvltp+ife le++ +G+ggeiqltDa++ ll++e++la++ +g+r+D+G+klgylka
  lcl|FitnessBrowser__HerbieS:HSERO_RS13375 208 VGRYVLTPAIFERLENIGTGAGGEIQLTDAISALLQQEQILAYRYEGQRFDCGSKLGYLKA 268
                                                ***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (335 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: 12.87
//
[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