Alignments for a candidate for hutG in Cupriavidus basilensis 4G11

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.22936.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.49
//
[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