GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sinorhizobium meliloti 1021

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate SM_b21633 SM_b21633 enoyl-CoA hydratase

Query= curated2:P24162
         (257 letters)



>FitnessBrowser__Smeli:SM_b21633
          Length = 263

 Score =  221 bits (562), Expect = 2e-62
 Identities = 127/262 (48%), Positives = 161/262 (61%), Gaps = 13/262 (4%)

Query: 5   TIRYEISEGLAVITLDRPEVMNALNAAMRHELTAALHRARGE--ARAIVLTGSGRAFCSG 62
           T+   +  G+  +TL+RP+ +NA N  M   L A   RAR +   RA++LTG+GR F +G
Sbjct: 6   TVLSALEAGVLRLTLNRPDKLNAFNEEMHLALRAGFERARSDDDVRAVMLTGAGRGFSAG 65

Query: 63  QDLGD------GAAE-GLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLALA 115
           QDLGD      GA + G  +ET     Y PLL+ I S   PV+ AVNG AAGAGAN+A A
Sbjct: 66  QDLGDRDPRKGGAPDLGRTIETF----YNPLLRLIRSLEKPVVCAVNGVAAGAGANIAFA 121

Query: 116 ADVVIAAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGL 175
            D+ +AA+SA F+QAF +IGL+PD+GGTW LPR VG ARA  +A+ AE + AE AA  GL
Sbjct: 122 CDITLAARSARFIQAFAKIGLVPDSGGTWSLPRLVGEARAKALAMTAEPLDAETAASWGL 181

Query: 176 IWEAVPDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQ 235
           IW AV D        A A  LA GP+      K+A  A  ++    QL LE  LQ E G+
Sbjct: 182 IWRAVDDAALMDEASALAVRLAAGPTRGLGLTKRAIQAAATHSFDEQLDLERDLQREAGR 241

Query: 236 SADFREGVQAFLEKRPPHFTGR 257
           SAD+ EGV AFL+KR P F GR
Sbjct: 242 SADYAEGVTAFLDKRNPEFRGR 263


Lambda     K      H
   0.321    0.133    0.397 

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: 159
Number of extensions: 6
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: 257
Length of database: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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: 47 (22.7 bits)

Align candidate SM_b21633 SM_b21633 (enoyl-CoA hydratase)
to HMM TIGR02280 (paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17))

# 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/TIGR02280.hmm
# target sequence database:        /tmp/gapView.8733.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02280  [M=256]
Accession:   TIGR02280
Description: PaaB1: phenylacetate degradation probable enoyl-CoA hydratase PaaB
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.6e-143  462.1   4.7   2.9e-143  461.9   4.7    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21633  SM_b21633 enoyl-CoA hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21633  SM_b21633 enoyl-CoA hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.9   4.7  2.9e-143  2.9e-143       1     256 []       7     263 .]       7     263 .] 0.99

  Alignments for each domain:
  == domain 1  score: 461.9 bits;  conditional E-value: 2.9e-143
                            TIGR02280   1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvtkgaapd 73 
                                          +l++le+gvlrltlnrpdkln+f+eemh +l++++er+++dd vra++ltGaGrGf+aGqdl++r+++kg+apd
  lcl|FitnessBrowser__Smeli:SM_b21633   7 VLSALEAGVLRLTLNRPDKLNAFNEEMHLALRAGFERARSDDdVRAVMLTGAGRGFSAGQDLGDRDPRKGGAPD 80 
                                          799*************************************999******************************* PP

                            TIGR02280  74 lGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlipdsGGtwllpr 147
                                          lG+t+e+fynpl+r++++l+kpvv+avnGvaaGaGan+a+a+di+laa+sa+fiqafak+Gl+pdsGGtw+lpr
  lcl|FitnessBrowser__Smeli:SM_b21633  81 LGRTIETFYNPLLRLIRSLEKPVVCAVNGVAAGAGANIAFACDITLAARSARFIQAFAKIGLVPDSGGTWSLPR 154
                                          ************************************************************************** PP

                            TIGR02280 148 lvGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrglalikralqaaetnsldtq 221
                                          lvG+arak+la+++e+ldaetaa+wGliw++vdd+al+de++ala++la++ptrgl+l+kra+qaa+t+s+d+q
  lcl|FitnessBrowser__Smeli:SM_b21633 155 LVGEARAKALAMTAEPLDAETAASWGLIWRAVDDAALMDEASALAVRLAAGPTRGLGLTKRAIQAAATHSFDEQ 228
                                          ************************************************************************** PP

                            TIGR02280 222 ldlerdlqrelGrsadyaeGvaafldkrepefkGk 256
                                          ldlerdlqre+GrsadyaeGv+afldkr+pef+G+
  lcl|FitnessBrowser__Smeli:SM_b21633 229 LDLERDLQREAGRSADYAEGVTAFLDKRNPEFRGR 263
                                          *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (263 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 7.30
//
[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