GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Cupriavidus basilensis 4G11

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS21770 RR42_RS21770 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Cup4G11:RR42_RS21770
          Length = 466

 Score =  531 bits (1367), Expect = e-155
 Identities = 264/461 (57%), Positives = 344/461 (74%), Gaps = 1/461 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FDLIV+GGGPGGYVAAIRA QL +K ALVE+ HLGGICLNWGCIPTK+LLRSA+V   ++
Sbjct: 6   FDLIVVGGGPGGYVAAIRATQLGMKTALVEKAHLGGICLNWGCIPTKALLRSADVLRLVK 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +A AYG+ +  P  DL  ++ARSR VA +L  GV  L++KN V V++G G+L G  ++ V
Sbjct: 66  DAAAYGVHAAPPTADLPAMVARSRAVAAQLNKGVAHLMKKNGVTVLNGHGRLAGKGKLEV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
             T+G+ +I+ +  I++ATGARARQLP + +DGK +WTY  AL PP +PK++L++G+GAI
Sbjct: 126 TATDGKTRIVSSAHILLATGARARQLPALPADGKTVWTYRDALAPPVVPKRMLIVGAGAI 185

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           GIEFASFY   GAEV++VE A +ILP+EDA++ A VA +  + GI + T + +Q+     
Sbjct: 186 GIEFASFYRAVGAEVTVVEMAQRILPVEDADICAQVASSLTREGIVLHTGTGIQSAERKG 245

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
           +G + E+ G      +      +VA G+V NVE++GL++  +K+++  I  DGFGRT+  
Sbjct: 246 QGWSIELQGGKSGGARVDVDVVLVAAGIVGNVEDLGLERTAVKVEKTHIVTDGFGRTDEP 305

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
            V+AIGDVAG P LAHKASH+GVI  E IAG  H H L+   IP CTY+ PQVASVGLTE
Sbjct: 306 GVYAIGDVAGPPWLAHKASHEGVICVERIAGL-HPHALDATRIPACTYSHPQVASVGLTE 364

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
            +AR++G+ VK+G FPF  NGKAIA G+T G VK VFDA SG LLGAHMVG EVTEMIQG
Sbjct: 365 AQARERGHPVKVGKFPFAGNGKAIAMGSTAGLVKVVFDAGSGELLGAHMVGDEVTEMIQG 424

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           Y +A+TLETTEA++M  + PHPT+SEAMHE+VLAAYGRALH
Sbjct: 425 YAIAQTLETTEADLMAAVLPHPTMSEAMHEAVLAAYGRALH 465


Lambda     K      H
   0.319    0.135    0.393 

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: 630
Number of extensions: 18
Number of successful extensions: 2
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate RR42_RS21770 RR42_RS21770 (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.14700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-165  535.5   3.6   5.7e-165  535.4   3.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21770  RR42_RS21770 dihydrolipoamide de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21770  RR42_RS21770 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.4   3.6  5.7e-165  5.7e-165       2     461 .]       6     466 .]       5     466 .] 0.98

  Alignments for each domain:
  == domain 1  score: 535.4 bits;  conditional E-value: 5.7e-165
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               +d++v+GgGpgGYvaAira qlg+k+alvek +lGG+Cln+GCiPtKalL+sa+v++ +k+a+ +g+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770   6 FDLIVVGGGPGGYVAAIRATQLGMKTALVEKAHLGGICLNWGCIPTKALLRSADVLRLVKDAAAYGVHA 74 
                                               8******************************************************************** PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiA 138
                                               +  + dl ++++r+++v  +l++Gv++L+kkn+v+v++G+++l +k+++ev++++++ + ++  +i++A
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770  75 APPTADLPAMVARSRAVAAQLNKGVAHLMKKNGVTVLNGHGRLAGKGKLEVTATDGKtRIVSSAHILLA 143
                                               ****************************************************99987688899****** PP

                                 TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                               tG++ r+lp  l +d+k+v+t+++al+ + vp++++ivG+G+iG+Efas+++ +G++vtv+e+++rilp
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770 144 TGARARQLPA-LPADGKTVWTYRDALAPPVVPKRMLIVGAGAIGIEFASFYRAVGAEVTVVEMAQRILP 211
                                               **********.********************************************************** PP

                                 TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleel 274
                                               ++da+++ +++++l+++g+ ++t++ +++ e++ +  ++e +++      ++++ vLva G   n+e+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770 212 VEDADICAQVASSLTREGIVLHTGTGIQSAERKGQGWSIELQGGksGGARVDVDVVLVAAGIVGNVEDL 280
                                               ****************************99999999998877763356899****************** PP

                                 TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavP 343
                                               gle++ v++++   i++d   rt  pg+yaiGDv+g++ LAh+As+egv+++e+iag +++++d++ +P
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770 281 GLERTAVKVEK-THIVTDGFGRTDEPGVYAIGDVAGPPWLAHKASHEGVICVERIAGLHPHALDATRIP 348
                                               *********99.77******************************************************* PP

                                 TIGR01350 344 sviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgae 412
                                               +++y++P+vasvGlte+qa+e+g+ vkvgkfpfa ngka+a++ t G+vkv++d  +ge+lGah+vg e
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770 349 ACTYSHPQVASVGLTEAQARERGHPVKVGKFPFAGNGKAIAMGSTAGLVKVVFDAGSGELLGAHMVGDE 417
                                               ********************************************************************* PP

                                 TIGR01350 413 aseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               ++e+i+  a+a +le+t+ +l++++ pHPt+sEa++ea+laa+g+a+h+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21770 418 VTEMIQGYAIAQTLETTEADLMAAVLPHPTMSEAMHEAVLAAYGRALHI 466
                                               *********************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.45
//
[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