GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc02487 SMc02487 dihydrolipoamide dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>FitnessBrowser__Smeli:SMc02487
          Length = 468

 Score =  550 bits (1418), Expect = e-161
 Identities = 270/465 (58%), Positives = 347/465 (74%), Gaps = 2/465 (0%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+++IG GPGGYV AIKAAQLG+K   +EKR   GGTCLNVGCIPSKALLH+S M+H+A+
Sbjct: 4   DLIVIGSGPGGYVCAIKAAQLGMKVAVVEKRSTYGGTCLNVGCIPSKALLHASEMFHQAQ 63

Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164
           H     GV+V++ +++L  M+A KD  VK+   GV  LFKKNK++  +G GK L   +VS
Sbjct: 64  HGLEALGVEVANPKLNLQKMMAHKDATVKSNVDGVSFLFKKNKIDGFQGTGKVLGQGKVS 123

Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGITI--DEKKIVSSTGALSLTEIPKKLIVIGA 222
           V    GE  V++ K++++ATGSDV  +PG+ +  DEK IVSSTGAL+L ++P  +IV+G 
Sbjct: 124 VTNEKGEEQVLEAKNVVIATGSDVAGIPGVEVAFDEKTIVSSTGALALEKVPASMIVVGG 183

Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVD 282
           G IGLE+GSVW RLG++VTVVEF   I+  MDGE+ KQ QR L KQ + F L  KV G  
Sbjct: 184 GVIGLELGSVWARLGAKVTVVEFLDTILGGMDGEVAKQLQRMLTKQGIDFKLGAKVTGAV 243

Query: 283 SSGDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERF 342
            SGDG K+  EP +GGE TTL+A+VVL++ GR P T GL L K GV  D  GR+ ++  F
Sbjct: 244 KSGDGAKVTFEPVKGGEATTLDAEVVLIATGRKPSTDGLGLAKAGVVLDSRGRVEIDRHF 303

Query: 343 STNVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVG 402
            T+++GVYAIGDV+ GPMLAHKAE++GVA  E IAG+ GHV+YD +PGVVYT PEVASVG
Sbjct: 304 QTSIAGVYAIGDVVRGPMLAHKAEDEGVAVAEIIAGQAGHVNYDVIPGVVYTQPEVASVG 363

Query: 403 KTEEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGEL 462
           KTEE+LK  GV+Y +GKFPF AN RA+A+   +G VKILADKETD++LG HI+   AGE+
Sbjct: 364 KTEEELKAAGVAYKIGKFPFTANGRARAMLQTDGFVKILADKETDRVLGGHIIGFGAGEM 423

Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507
           IHE  + + +  SSED+ R CHAHPTMSEA+KEAA++T+ KPIHM
Sbjct: 424 IHEIAVLMEFGGSSEDLGRTCHAHPTMSEAVKEAALSTFFKPIHM 468


Lambda     K      H
   0.315    0.134    0.376 

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: 666
Number of extensions: 31
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: 507
Length of database: 468
Length adjustment: 34
Effective length of query: 473
Effective length of database: 434
Effective search space:   205282
Effective search space used:   205282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate SMc02487 SMc02487 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

# 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/TIGR01350.hmm
# target sequence database:        /tmp/gapView.27803.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01350  [M=461]
Accession:   TIGR01350
Description: lipoamide_DH: dihydrolipoyl dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-185  602.6  15.4   2.6e-185  602.4  15.4    1.0  1  lcl|FitnessBrowser__Smeli:SMc02487  SMc02487 dihydrolipoamide dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02487  SMc02487 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.4  15.4  2.6e-185  2.6e-185       2     461 .]       3     468 .]       2     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 602.4 bits;  conditional E-value: 2.6e-185
                           TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenvk 74 
                                         yd++viG+GpgGYv+Ai+aaqlg+kva+vek +++GGtClnvGCiP+KalL+++e+++++++ ++ lg+ev+n k
  lcl|FitnessBrowser__Smeli:SMc02487   3 YDLIVIGSGPGGYVCAIKAAQLGMKVAVVEKrSTYGGTCLNVGCIPSKALLHASEMFHQAQHgLEALGVEVANPK 77 
                                         9******************************999***************************************** PP

                           TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelpl 148
                                         l+l+k++++k+++vk+ v+Gv++L+kknk++ ++G++k+l++++v+v++ek+e ++leakn++iAtGs+++ +p+
  lcl|FitnessBrowser__Smeli:SMc02487  78 LNLQKMMAHKDATVKSNVDGVSFLFKKNKIDGFQGTGKVLGQGKVSVTNEKGEeQVLEAKNVVIATGSDVAGIPG 152
                                         **************************************************9988999****************** PP

                           TIGR01350 149 k.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklk 222
                                           +++dek++++s++al+l++vp s+++vGgGviG+E++s++a+lG+kvtv+e+ld+il  +d ev+k+l+++l+
  lcl|FitnessBrowser__Smeli:SMc02487 153 VeVAFDEKTIVSSTGALALEKVPASMIVVGGGVIGLELGSVWARLGAKVTVVEFLDTILGGMDGEVAKQLQRMLT 227
                                         99999********************************************************************** PP

                           TIGR01350 223 kkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdee 294
                                         k+g++++ +akvt    + + ++v++e  k+ e++tl+ae vL+a Grkp++++lgl+k gv ld+rg++++d++
  lcl|FitnessBrowser__Smeli:SMc02487 228 KQGIDFKLGAKVTgaVKSGDGAKVTFEPVKGgEATTLDAEVVLIATGRKPSTDGLGLAKAGVVLDSRGRVEIDRH 302
                                         *************7333445567778877777******************************************* PP

                           TIGR01350 295 lrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegiev 369
                                         ++t+++g+yaiGDv++++mLAh+A++egv +ae iag++  +++y+++P v+yt+PevasvG+tee++k++g+++
  lcl|FitnessBrowser__Smeli:SMc02487 303 FQTSIAGVYAIGDVVRGPMLAHKAEDEGVAVAEIIAGQAG-HVNYDVIPGVVYTQPEVASVGKTEEELKAAGVAY 376
                                         *************************************998.9********************************* PP

                           TIGR01350 370 kvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtls 444
                                         k+gkfpf+ang+a+a+ +tdGfvk+++dk+t+++lG hi+g  a e+i+e+a+++e+++++e+l +t+h+HPt+s
  lcl|FitnessBrowser__Smeli:SMc02487 377 KIGKFPFTANGRARAMLQTDGFVKILADKETDRVLGGHIIGFGAGEMIHEIAVLMEFGGSSEDLGRTCHAHPTMS 451
                                         *************************************************************************** PP

                           TIGR01350 445 Eaikeaalaalgkaihv 461
                                         Ea+keaal+++ k+ih+
  lcl|FitnessBrowser__Smeli:SMc02487 452 EAVKEAALSTFFKPIHM 468
                                         ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.47
//
[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