Alignments for a candidate for lpd in Cupriavidus basilensis 4G11

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.7341.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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.50
//
[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