GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Sinorhizobium meliloti 1021

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate SMc03206 SMc03206 maleylacetoacetate isomerase (glutathione transferase zeta 1) protein

Query= reanno::psRCH2:GFF3446
         (219 letters)



>FitnessBrowser__Smeli:SMc03206
          Length = 217

 Score =  172 bits (437), Expect = 3e-48
 Identities = 100/214 (46%), Positives = 135/214 (63%), Gaps = 6/214 (2%)

Query: 1   MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60
           +  E  LY YWRSSA+YRVRIALNL G AYR VPV L+      RA ++ A NPQ LVP+
Sbjct: 5   VANETVLYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAKA--HRAPEHLARNPQGLVPV 62

Query: 61  LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120
           L  +G    R++QSLAI+EYL E      LLPA P++R +VR+L+  +A +IHP+ NL V
Sbjct: 63  LDIDGE---RLTQSLAIIEYLAETRDGTGLLPAHPIDRQRVRALSYAVAMDIHPVCNLGV 119

Query: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLE-TFGDKLSLNDRPGYLEACLVPQVY 179
           +  + A  G  + A+  W + ++ +GLAA E+ L+          DRP   + CLVPQVY
Sbjct: 120 VARVMAGAGDGEAARREWMQKFIGEGLAAFERMLDHPATGAFCHGDRPTMADLCLVPQVY 179

Query: 180 NARRFACDLAAYPRILEIVARCETLPAFQQAAPE 213
           NARR+  DLAA P ++ I  RC  + AFQ+A P+
Sbjct: 180 NARRWDVDLAACPLLVAIDRRCAGIDAFQRAHPD 213


Lambda     K      H
   0.321    0.137    0.412 

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: 172
Number of extensions: 7
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: 219
Length of database: 217
Length adjustment: 22
Effective length of query: 197
Effective length of database: 195
Effective search space:    38415
Effective search space used:    38415
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: 45 (21.9 bits)

Align candidate SMc03206 SMc03206 (maleylacetoacetate isomerase (glutathione transferase zeta 1) protein)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

# 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/TIGR01262.hmm
# target sequence database:        /tmp/gapView.12228.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01262  [M=211]
Accession:   TIGR01262
Description: maiA: maleylacetoacetate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.8e-89  284.3   0.0    3.1e-89  284.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03206  SMc03206 maleylacetoacetate isom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03206  SMc03206 maleylacetoacetate isomerase (glutathione transferase zeta 1) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   0.0   3.1e-89   3.1e-89       2     208 ..      11     216 ..      10     217 .] 0.98

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 3.1e-89
                           TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLeet 76 
                                         lY+y+rSsasyRvRiaL+L+g +y+svpv+Ll++ +++++e+ a+NPq+lvP+L+id ge+ltqSlAiieyL et
  lcl|FitnessBrowser__Smeli:SMc03206  11 LYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAK-AHRAPEHLARNPQGLVPVLDID-GERLTQSLAIIEYLAET 83 
                                         9********************************7.**********************.6**************** PP

                           TIGR01262  77 ypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk.eka 150
                                         ++ + Llp++p +r+rvral++++a+dihP++Nl v++++++ +g  e++++ew++++i +Glaa+E++l+ +++
  lcl|FitnessBrowser__Smeli:SMc03206  84 RDGTGLLPAHPIDRQRVRALSYAVAMDIHPVCNLGVVARVMAGAGDGEAARREWMQKFIGEGLAAFERMLDhPAT 158
                                         ***********************************************************************999* PP

                           TIGR01262 151 gafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqp 208
                                         gafc+Gd++t+ad+cLvpqvynA+r++vdla++P+l +i++++a ++afq+ahp++++
  lcl|FitnessBrowser__Smeli:SMc03206 159 GAFCHGDRPTMADLCLVPQVYNARRWDVDLAACPLLVAIDRRCAGIDAFQRAHPDRAK 216
                                         ******************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (217 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: 6.34
//
[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