GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutG in Cupriavidus basilensis 4G11

Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate RR42_RS14625 RR42_RS14625 formimidoylglutamase

Query= reanno::Koxy:BWI76_RS08725
         (318 letters)



>FitnessBrowser__Cup4G11:RR42_RS14625
          Length = 312

 Score =  244 bits (624), Expect = 1e-69
 Identities = 150/310 (48%), Positives = 184/310 (59%), Gaps = 8/310 (2%)

Query: 8   PAALWQGRDDSAEAANALRLFQTIVRAERFEPEMLAGDIALLGFACDEGVRRNKGRTGAE 67
           P ++W+GR D+ E  +  RLF  +VRA+    E + G   LLGF CD GV RN GR GA 
Sbjct: 5   PGSIWRGRSDAGELGDTRRLFH-VVRAQG--AERVPGAPVLLGFCCDAGVLRNLGRPGAA 61

Query: 68  RGPETLRRALANMASHDGHDRCVDMGTIHVADDALEAAQQALREAVTACQRAGKRTLVLG 127
            GP  +RRALA + +H G     D G +   D  LE AQQAL  AV A    G   LVLG
Sbjct: 62  GGPREIRRALAGIPAH-GLAAFHDAGDVVCHDGDLETAQQALATAVAAELAQGAFPLVLG 120

Query: 128 GGHETAFGHGAGV---LDAFPGE-EVGIINLDAHLDLRIADRASSGTPFRQLALACEAQR 183
           GGHE A+G   G+   LDA      V +INLDAH DLR     SSGTPF Q+A AC  + 
Sbjct: 121 GGHEIAWGTWQGLRAHLDARGDHGRVLVINLDAHFDLRTGRPGSSGTPFDQIAQACHERG 180

Query: 184 RAFHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELARNIARYDRLYL 243
           + F YAC+GVSR  NT AL   A   GV  +ED+ +        + EL   +   D +YL
Sbjct: 181 QRFEYACLGVSRLGNTAALFAHAQALGVHYVEDVQMQERHLDARLAELQGLMDAVDHVYL 240

Query: 244 TIDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEFNPQYDIDSQGA 303
           TIDLDVLPA  MPAVSAPA  G+PL  +  +V  +  SGKL+  DL EFNP YD D+ GA
Sbjct: 241 TIDLDVLPAAVMPAVSAPAPYGVPLPVVEEVVALVRASGKLRVADLAEFNPLYDRDACGA 300

Query: 304 RAAARLAWQI 313
           RAAARLA+++
Sbjct: 301 RAAARLAYRL 310


Lambda     K      H
   0.322    0.135    0.408 

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: 327
Number of extensions: 15
Number of successful extensions: 4
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: 318
Length of database: 312
Length adjustment: 27
Effective length of query: 291
Effective length of database: 285
Effective search space:    82935
Effective search space used:    82935
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS14625 RR42_RS14625 (formimidoylglutamase)
to HMM TIGR01227 (hutG: formimidoylglutamase (EC 3.5.3.8))

# 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/TIGR01227.hmm
# target sequence database:        /tmp/gapView.5142.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01227  [M=307]
Accession:   TIGR01227
Description: hutG: formimidoylglutamase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.9e-91  290.1   0.1    1.1e-90  289.9   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS14625  RR42_RS14625 formimidoylglutamas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14625  RR42_RS14625 formimidoylglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.9   0.1   1.1e-90   1.1e-90       1     304 [.       9     309 ..       9     312 .] 0.95

  Alignments for each domain:
  == domain 1  score: 289.9 bits;  conditional E-value: 1.1e-90
                                 TIGR01227   1 lqgrldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairqala 69 
                                               + gr d  e ++ rr ++v++ +       +  + +++l+G+ +d+gv rn Gr GA  +P  ir+ala
  lcl|FitnessBrowser__Cup4G11:RR42_RS14625   9 WRGRSDAGELGDTRRLFHVVRAQGA-----ERVPGAPVLLGFCCDAGVLRNLGRPGAAGGPREIRRALA 72 
                                               7889999999999999999988877.....455889********************************* PP

                                 TIGR01227  70 nlgdlvasealyDlGdivlegddlvdaqkevaqavaelladarvvvllGGdneiayatikalaqa..ak 136
                                               +   ++   a  D+Gd+v++++dl+ aq+++a ava+ la+++ +++lGG++eia+ t ++l+++  a+
  lcl|FitnessBrowser__Cup4G11:RR42_RS14625  73 GI-PAHGLAAFHDAGDVVCHDGDLETAQQALATAVAAELAQGAFPLVLGGGHEIAWGTWQGLRAHldAR 140
                                               **.6678899*******************************************************8877 PP

                                 TIGR01227 137 gek.riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivlGirrfsntqalfdyakkkg 202
                                               g++ r+ vin+DAHfDlR+      +sGTpf q+++++ + +  f++++lG++r++nt+alf++a+ +g
  lcl|FitnessBrowser__Cup4G11:RR42_RS14625 141 GDHgRVLVINLDAHFDLRTGR--PGSSGTPFDQIAQACHERGqrFEYACLGVSRLGNTAALFAHAQALG 207
                                               66689*************988..889****************999************************ PP

                                 TIGR01227 203 vryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPGvsApaagGleleellelvkria 271
                                               v+yv+d +++e +l+  ++ l+ ++d vD++ylt+dlDVl+aa  P vsApa+ G+ l++++e+v  + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14625 208 VHYVEDVQMQERHLDARLAELQGLMDAVDHVYLTIDLDVLPAAVMPAVSAPAPYGVPLPVVEEVVALVR 276
                                               ********************************************************************* PP

                                 TIGR01227 272 asdkvrgveivEvnPtlDaddrTarlaArlvah 304
                                               as+k+r+++++E+nP +D d   ar+aArl   
  lcl|FitnessBrowser__Cup4G11:RR42_RS14625 277 ASGKLRVADLAEFNPLYDRDACGARAAARLAYR 309
                                               *****************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (312 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: 6.88
//
[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:

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:

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:

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:

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