GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Marinobacter adhaerens HP15

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate GFF1848 HP15_1805 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__Marino:GFF1848
          Length = 264

 Score =  224 bits (570), Expect = 2e-63
 Identities = 119/263 (45%), Positives = 162/263 (61%), Gaps = 12/263 (4%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAG-RCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHV 59
           + +++IPAF DNYIW L+D A  + LIVDPG A+PVL+ +A N    + I +THHH DHV
Sbjct: 2   LTISAIPAFSDNYIWCLSDTASDKALIVDPGQAQPVLDHLAENGLTLDTILVTHHHPDHV 61

Query: 60  GGVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFS 119
           GGVK+L+ +FP   V GP ++  KG+T +V  G+        F V+  PGHTL HI YF+
Sbjct: 62  GGVKDLISRFPDCRVTGPADSPYKGSTNLVHPGDEVIWEDITFQVLGVPGHTLDHIAYFT 121

Query: 120 ------KPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMK 173
                 +P LFCGDTLF  GCGRLFEG+  QM QSL+ L ALP  T V CAHEYTL+N++
Sbjct: 122 DVEVNGRPVLFCGDTLFVCGCGRLFEGSPEQMRQSLQTLRALPGKTAVYCAHEYTLANLR 181

Query: 174 FALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTED---IDLINVINE 230
           FA S LP D  +  + ++ +  R   + T+P +L+NE+++N FLR +D   +D       
Sbjct: 182 FARSWLPEDEGLRTFEQECQAARDAGKPTVPSVLENEKRLNPFLRWDDPAVVDSARAYCS 241

Query: 231 ETLLQQPEER--FAWLRSKKDRF 251
              L    +   FA +R  KD F
Sbjct: 242 SRGLPADSDNAIFAAIRHGKDNF 264


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: 259
Number of extensions: 8
Number of successful extensions: 3
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 GFF1848 HP15_1805 (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.3912474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.9e-101  322.6   0.0   8.9e-101  322.4   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1848  HP15_1805 hydroxyacylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1848  HP15_1805 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.4   0.0  8.9e-101  8.9e-101       1     248 []       4     264 .]       4     264 .] 0.98

  Alignments for each domain:
  == domain 1  score: 322.4 bits;  conditional E-value: 8.9e-101
                           TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.vkvvg 73 
                                         i aipa+sdNyiw+l+d++s +a++vDpg+a+pvl++l+e+gl+l++il+THhH DHvggv++l+++fp ++v+g
  lcl|FitnessBrowser__Marino:GFF1848   4 ISAIPAFSDNYIWCLSDTASdKALIVDPGQAQPVLDHLAENGLTLDTILVTHHHPDHVGGVKDLISRFPdCRVTG 78 
                                         678*****************9****************************************************** PP

                           TIGR03413  74 paeeripgltkevkegdevellelevevlevpGHtlgHiayyleee....kvlFcgDtLfsaGCGrlfegtaeqm 144
                                         pa++  +g t+ v+ gdev + + +++vl vpGHtl+Hiay+++ e    +vlFcgDtLf +GCGrlfeg++eqm
  lcl|FitnessBrowser__Marino:GFF1848  79 PADSPYKGSTNLVHPGDEVIWEDITFQVLGVPGHTLDHIAYFTDVEvngrPVLFCGDTLFVCGCGRLFEGSPEQM 153
                                         ******************************************99878899************************* PP

                           TIGR03413 145 leslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLrae 219
                                          +slq l+aLp +t+vycaHEYtl+NlrFa++  pe+e l++  +e++a+r++gkpt+Ps l++ek+ NpFLr++
  lcl|FitnessBrowser__Marino:GFF1848 154 RQSLQTLRALPGKTAVYCAHEYTLANLRFARSWLPEDEGLRTFEQECQAARDAGKPTVPSVLENEKRLNPFLRWD 228
                                         *************************************************************************** PP

                           TIGR03413 220 eaevkaalee.......ekaeevevfaelRekkdkf 248
                                         +++v  ++++        ++++ ++fa++R+ kd+f
  lcl|FitnessBrowser__Marino:GFF1848 229 DPAVVDSARAycssrglPADSDNAIFAAIRHGKDNF 264
                                         ****999998999999999999************98 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.77
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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