GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate HSERO_RS14875 HSERO_RS14875 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__HerbieS:HSERO_RS14875
          Length = 475

 Score =  514 bits (1325), Expect = e-150
 Identities = 270/476 (56%), Positives = 338/476 (71%), Gaps = 7/476 (1%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS+ FDVVVIG GPGGY+AAIRAAQLG  TACI+++  ++G  A GGTC NVGCIPSKAL
Sbjct: 1   MSKNFDVVVIGGGPGGYIAAIRAAQLGFNTACIDEWKNEKGGPAPGGTCTNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           L SS  Y  A   F  HGIE KG+ +++  M+ RK  +VK    GI  LFK N V+ F G
Sbjct: 61  LQSSEHYEHASHGFAEHGIEVKGLGLNLEKMLGRKNTVVKQNNDGILYLFKKNKVSFFHG 120

Query: 121 HGKLLANK----QVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALE 176
            G  +       +++V G   +T  + A++VI+A+GS    +P A   + +I+ +TGAL 
Sbjct: 121 RGSFVKGDANGYEIKVAGAAEET--ITAKHVIVATGSNARALPGAEFDEKLILSNTGALS 178

Query: 177 FQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQG 236
              VPKKLGVIGAGVIGLE+GSVW RLGAEVTVLEAL  FL A DEQIAKEA K+LTKQG
Sbjct: 179 ITEVPKKLGVIGAGVIGLEMGSVWRRLGAEVTVLEALPTFLGAVDEQIAKEAQKLLTKQG 238

Query: 237 LNIRLGARVTASEVKKKQVTVTFTDANGEQKE-TFDKLIVAVGRRPVTTDLLAADSGVTL 295
           L + LG ++ A +  K  V+V +TDA G+     FDKLIV++GR P T  L A   G+ L
Sbjct: 239 LAVNLGVKIGAIKAGKNSVSVEYTDAKGDAHTGEFDKLIVSIGRTPNTIGLNAEGVGLKL 298

Query: 296 DERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPS 355
           DERGFI VD  CKT++P V+A+GDVVRG MLAHKA EEGV VAERIAG    +N++ IP 
Sbjct: 299 DERGFIAVDGDCKTNLPNVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHGHVNFNTIPW 358

Query: 356 VIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVL 415
           VIYT PEIAWVGKTEQ LKAEGV+   GTFPF A+GRA A  DT+G+VK +ADAKTD +L
Sbjct: 359 VIYTSPEIAWVGKTEQQLKAEGVQYKAGTFPFLANGRARALGDTSGMVKFLADAKTDEIL 418

Query: 416 GVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           GVH++GP A+EL+ +  + MEF  S+ED+  +  +HP+LSEA  EAALAV+  A++
Sbjct: 419 GVHIVGPMASELISEAVVAMEFRASSEDIARICHAHPSLSEATKEAALAVDKRALN 474


Lambda     K      H
   0.316    0.134    0.375 

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: 682
Number of extensions: 33
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: 478
Length of database: 475
Length adjustment: 33
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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: 51 (24.3 bits)

Align candidate HSERO_RS14875 HSERO_RS14875 (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.29443.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-166  540.9   4.1   1.4e-166  540.7   4.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS14875  HSERO_RS14875 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14875  HSERO_RS14875 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.7   4.1  1.4e-166  1.4e-166       1     460 [.       4     474 ..       4     475 .] 0.95

  Alignments for each domain:
  == domain 1  score: 540.7 bits;  conditional E-value: 1.4e-166
                                  TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevveelk 61 
                                                ++dvvviGgGpgGY+aAiraaqlg+++a++++  ++      GGtC+nvGCiP+KalL+s+e +e+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875   4 NFDVVVIGGGPGGYIAAIRAAQLGFNTACIDEwkNEkggpaPGGTCTNVGCIPSKALLQSSEHYEHAS 71 
                                                69****************************86532223333799************************ PP

                                  TIGR01350  62 e.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld....kkevevkke 124
                                                + ++e+giev+++ l+lek+l rk++vvk+ ++G+ +L+kknkv+ ++G++++++      e++v++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875  72 HgFAEHGIEVKGLGLNLEKMLGRKNTVVKQNNDGILYLFKKNKVSFFHGRGSFVKgdanGYEIKVAGA 139
                                                *****************************************************986655568999999 PP

                                  TIGR01350 125 kkekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifakl 192
                                                + e++++ak++i+AtGs+ r+lp+  e+dek+++++++al+++evp++l ++G+GviG+E++s++++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875 140 A-EETITAKHVIVATGSNARALPG-AEFDEKLILSNTGALSITEVPKKLGVIGAGVIGLEMGSVWRRL 205
                                                8.57********************.9****************************************** PP

                                  TIGR01350 193 Gvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetlea 258
                                                G++vtv+e+l++ l a+d++++k+++k l+k+g+ +  + k+ ++++ +++v+  ++  k++++t e 
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875 206 GAEVTVLEALPTFLGAVDEQIAKEAQKLLTKQGLAVNLGVKIGAIKAGKNSVSveYTDAKGDAHTGEF 273
                                                *******************************************999999999943444555899999* PP

                                  TIGR01350 259 ekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaa 326
                                                +k++v++Gr+pn+ +l+ e +g++lderg+i vd +++tn+p+++a+GDv++++mLAh+A++egv +a
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875 274 DKLIVSIGRTPNTIGLNAEGVGLKLDERGFIAVDGDCKTNLPNVWAVGDVVRGPMLAHKAEEEGVAVA 341
                                                ******************************************************************** PP

                                  TIGR01350 327 ekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkv 394
                                                e+iag++  +++ +++P viyt+Pe+a vG+te+q+k+eg+++k+g fpf ang+a+al++t+G+vk 
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875 342 ERIAGQHG-HVNFNTIPWVIYTSPEIAWVGKTEQQLKAEGVQYKAGTFPFLANGRARALGDTSGMVKF 408
                                                *****998.9********************************************************** PP

                                  TIGR01350 395 ivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                                ++d kt+eilG+hivg+ aselise+++a+e+++++e++a+++h+HP+lsEa+keaala+ ++a++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14875 409 LADAKTDEILGVHIVGPMASELISEAVVAMEFRASSEDIARICHAHPSLSEATKEAALAVDKRALN 474
                                                ***********************************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (475 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.24
//
[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