GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Herbaspirillum seropedicae SmR1

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate HSERO_RS17120 HSERO_RS17120 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__HerbieS:HSERO_RS17120
          Length = 264

 Score =  209 bits (531), Expect = 6e-59
 Identities = 119/265 (44%), Positives = 162/265 (61%), Gaps = 16/265 (6%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAGR-CLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHV 59
           +++ ++PAFDDNY+W+++D  GR   +VDPGDA PVL A+ A      AI LTHHH DHV
Sbjct: 1   LDVLAVPAFDDNYLWIIHD--GRYAAVVDPGDAVPVLAALQAEGLTLAAILLTHHHADHV 58

Query: 60  GGVKELVEK-----FPQIVVYGPQETQD--KGTTQVV--KDGETAFVLGHEFSVIATPGH 110
           GGV EL  +     FP I VYGP   Q   KG T  +   D     VLG    VI  PGH
Sbjct: 59  GGVVELARQAASDTFPIIPVYGPAREQSRIKGMTVPLHGNDQVDIAVLGLRLEVIEVPGH 118

Query: 111 TLGHICYFS--KPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYT 168
           T+GHI Y +  +  LFCGDTLF+GGCGRLFEGT  QM  SL +L++LP  T V CAHEYT
Sbjct: 119 TMGHIAYHAPEQAMLFCGDTLFAGGCGRLFEGTPQQMVDSLSRLASLPGQTAVYCAHEYT 178

Query: 169 LSNMKFALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVI 228
           LSN+KFA  + P +  ++    + +  R + + T+P  +  ERQ N FLR  + ++++ +
Sbjct: 179 LSNLKFAAEVEPGNAELHARITRERARRERGEPTVPTSIALERQTNPFLRATEKEILDSL 238

Query: 229 NEETLLQQPEE--RFAWLRSKKDRF 251
            +   L++ +E   FA LR  K+ +
Sbjct: 239 QKAGRLKELDEVSSFAALREWKNSY 263


Lambda     K      H
   0.321    0.138    0.425 

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: 218
Number of extensions: 13
Number of successful extensions: 5
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: 251
Length of database: 264
Length adjustment: 24
Effective length of query: 227
Effective length of database: 240
Effective search space:    54480
Effective search space used:    54480
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: 47 (22.7 bits)

Align candidate HSERO_RS17120 HSERO_RS17120 (hydroxyacylglutathione hydrolase)
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))

# 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/TIGR03413.hmm
# target sequence database:        /tmp/gapView.25171.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03413  [M=248]
Accession:   TIGR03413
Description: GSH_gloB: hydroxyacylglutathione hydrolase
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-102  327.8   0.0   2.3e-102  327.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17120  HSERO_RS17120 hydroxyacylglutath


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17120  HSERO_RS17120 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.6   0.0  2.3e-102  2.3e-102       2     248 .]       4     263 ..       3     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 327.6 bits;  conditional E-value: 2.3e-102
                                  TIGR03413   2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellek... 66 
                                                 a+pa++dNy+w+++d +  a+vvDpg+a pvl+al+++gl+l+aillTHhHaDHvggv el ++   
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120   4 LAVPAFDDNYLWIIHDGR-YAAVVDPGDAVPVLAALQAEGLTLAAILLTHHHADHVGGVVELARQaas 70 
                                                589**************9.9******************************************876222 PP

                                  TIGR03413  67 ..fp.vkvvgpaee..ripgltkevkegdevel..lelevevlevpGHtlgHiayyleeekvlFcgDt 127
                                                  fp ++v+gpa+e  ri+g+t++++ +d+v++  l+l++ev+evpGHt+gHiay+++e+ +lFcgDt
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120  71 dtFPiIPVYGPAREqsRIKGMTVPLHGNDQVDIavLGLRLEVIEVPGHTMGHIAYHAPEQAMLFCGDT 138
                                                225699******99999*************9987799******************************* PP

                                  TIGR03413 128 LfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealr 195
                                                Lf+ GCGrlfegt++qm++sl++la+Lp +t+vycaHEYtlsNl+Fa++vep n++l++r+++ +a+r
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120 139 LFAGGCGRLFEGTPQQMVDSLSRLASLPGQTAVYCAHEYTLSNLKFAAEVEPGNAELHARITRERARR 206
                                                ******************************************************************** PP

                                  TIGR03413 196 akgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248
                                                ++g+pt+P+++a e++tNpFLra e+e+  +l++    ++ +ev+ fa+lRe+k+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17120 207 ERGEPTVPTSIALERQTNPFLRATEKEILDSLQKagrlKELDEVSSFAALREWKNSY 263
                                                ****************************99999999999999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (264 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: 10.68
//
[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