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_RS31730 RR42_RS31730 formimidoylglutamase

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



>FitnessBrowser__Cup4G11:RR42_RS31730
          Length = 313

 Score =  258 bits (660), Expect = 1e-73
 Identities = 152/310 (49%), Positives = 192/310 (61%), Gaps = 12/310 (3%)

Query: 10  ALWQGRDDSAEAANALRLFQTIVRAERFEPEMLAGDIALLGFACDEGVRRNKGRTGAERG 69
           ++WQGR D+ E  +  RLF  +  A    P   AG   ++GFACD GV RN GR GA +G
Sbjct: 8   SVWQGRSDAGERGDTRRLFHVVRAAGAPLP---AGSPVVVGFACDAGVLRNHGRAGAAQG 64

Query: 70  PETLRRALANMASHDGHDRCVDMGTIHVADDALEAAQQALREAVTACQRAGKRTLVLGGG 129
           P+ +RRALAN+ +H G     D G +   DDALEAAQ+ L  AV A    G   LVLGGG
Sbjct: 65  PDAIRRALANVPAH-GLPALYDAGNVICEDDALEAAQERLAGAVRAVLDGGGLPLVLGGG 123

Query: 130 HETAFGHGAGV---LDAF-PGEEVGIINLDAHLDLRIADRASSGTPFRQLALACEAQRRA 185
           HE A+G   G+   LDA   G  + I+N+DAH DLR +  ASSGTPF Q+A  CE+ RR 
Sbjct: 124 HEVAWGSWQGLRAHLDAAGDGGRLLIVNIDAHFDLRTSRPASSGTPFDQIA--CESARRG 181

Query: 186 --FHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELARNIARYDRLYL 243
             F Y C+GVSR ANT AL   A   GV+ +ED+D+        +  L   +A  + +YL
Sbjct: 182 LPFDYVCLGVSRLANTPALFARADELGVSYVEDVDLQERHLDARLAALRERMALAEHVYL 241

Query: 244 TIDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEFNPQYDIDSQGA 303
           TIDLD LPA  MP VSAPAA G+PLA +  +V  + RSGKL+  DL E+NP YD D QGA
Sbjct: 242 TIDLDALPAAVMPGVSAPAAFGVPLAVVEALVGEVRRSGKLRVADLAEYNPSYDRDHQGA 301

Query: 304 RAAARLAWQI 313
           R AARLA+++
Sbjct: 302 RVAARLAYRL 311


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: 328
Number of extensions: 20
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: 313
Length adjustment: 27
Effective length of query: 291
Effective length of database: 286
Effective search space:    83226
Effective search space used:    83226
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_RS31730 RR42_RS31730 (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.24174.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.1e-88  282.5   0.0    2.3e-88  282.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS31730  RR42_RS31730 formimidoylglutamas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS31730  RR42_RS31730 formimidoylglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.3   0.0   2.3e-88   2.3e-88       1     306 [.      10     312 ..      10     313 .] 0.95

  Alignments for each domain:
  == domain 1  score: 282.3 bits;  conditional E-value: 2.3e-88
                                 TIGR01227   1 lqgrldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairqala 69 
                                               +qgr d  e ++ rr ++v++     +l+       ++++G+a+d+gv rn+Gr GA ++P+air+ala
  lcl|FitnessBrowser__Cup4G11:RR42_RS31730  10 WQGRSDAGERGDTRRLFHVVRAAGA-PLP----AGSPVVVGFACDAGVLRNHGRAGAAQGPDAIRRALA 73 
                                               99*****************998877.663....45699******************************* PP

                                 TIGR01227  70 nlgdlvasealyDlGdivlegddlvdaqkevaqavaelladarvvvllGGdneiayatikalaqa..ak 136
                                               n   ++   alyD+G++ +e+d l++aq+ +a av+++l+ + ++++lGG++e+a+ + ++l+++  a 
  lcl|FitnessBrowser__Cup4G11:RR42_RS31730  74 NV-PAHGLPALYDAGNVICEDDALEAAQERLAGAVRAVLDGGGLPLVLGGGHEVAWGSWQGLRAHldAA 141
                                               **.5667789*******************************************************7755 PP

                                 TIGR01227 137 gek.riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivlGirrfsntqalfdyakkkg 202
                                               g+  r  ++n+DAHfDlR+     ++sGTpf q++ e    +  f +++lG++r+ nt+alf++a+++g
  lcl|FitnessBrowser__Cup4G11:RR42_RS31730 142 GDGgRLLIVNIDAHFDLRTSR--PASSGTPFDQIACESARRGlpFDYVCLGVSRLANTPALFARADELG 208
                                               5547999***********998..9********************************************* PP

                                 TIGR01227 203 vryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPGvsApaagGleleellelvkria 271
                                               v+yv+d  l+e +l+  +++l+e +   +++ylt+dlD l+aa  PGvsApaa G+ l ++++lv  + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS31730 209 VSYVEDVDLQERHLDARLAALRERMALAEHVYLTIDLDALPAAVMPGVSAPAAFGVPLAVVEALVGEVR 277
                                               ********************************************************************* PP

                                 TIGR01227 272 asdkvrgveivEvnPtlDaddrTarlaArlvahll 306
                                               +s+k+r+++++E+nP++D d++ ar+aArl   ll
  lcl|FitnessBrowser__Cup4G11:RR42_RS31730 278 RSGKLRVADLAEYNPSYDRDHQGARVAARLAYRLL 312
                                               *****************************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (313 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: 8.05
//
[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