Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

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.12676.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.92
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources