Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

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.2211091.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  FitnessBrowser__HerbieS:HSERO_RS14875  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS14875  
   #    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.....lGGtClnvGCiPtKalLksaevveelke.ak 64 
                                            ++dvvviGgGpgGY+aAiraaqlg+++a++++  ++      GGtC+nvGCiP+KalL+s+e +e++++ ++
  FitnessBrowser__HerbieS:HSERO_RS14875   4 NFDVVVIGGGPGGYIAAIRAAQLGFNTACIDEwkNEkggpaPGGTCTNVGCIPSKALLQSSEHYEHASHgFA 75 
                                            69****************************86532223333799**************************** PP

                              TIGR01350  65 elgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld....kkevevkkekkekklea 132
                                            e+giev+++ l+lek+l rk++vvk+ ++G+ +L+kknkv+ ++G++++++      e++v++ + e++++a
  FitnessBrowser__HerbieS:HSERO_RS14875  76 EHGIEVKGLGLNLEKMLGRKNTVVKQNNDGILYLFKKNKVSFFHGRGSFVKgdanGYEIKVAGAA-EETITA 146
                                            *************************************************9866555689999998.57**** PP

                              TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldr 204
                                            k++i+AtGs+ r+lp+  e+dek+++++++al+++evp++l ++G+GviG+E++s++++lG++vtv+e+l++
  FitnessBrowser__HerbieS:HSERO_RS14875 147 KHVIVATGSNARALPG-AEFDEKLILSNTGALSITEVPKKLGVIGAGVIGLEMGSVWRRLGAEVTVLEALPT 217
                                            ****************.9****************************************************** PP

                              TIGR01350 205 ilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleel 274
                                             l a+d++++k+++k l+k+g+ +  + k+ ++++ +++v+  ++  k++++t e +k++v++Gr+pn+ +l
  FitnessBrowser__HerbieS:HSERO_RS14875 218 FLGAVDEQIAKEAQKLLTKQGLAVNLGVKIGAIKAGKNSVSveYTDAKGDAHTGEFDKLIVSIGRTPNTIGL 289
                                            *******************************999999999943444555899999***************** PP

                              TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsvi 346
                                            + e +g++lderg+i vd +++tn+p+++a+GDv++++mLAh+A++egv +ae+iag++  +++ +++P vi
  FitnessBrowser__HerbieS:HSERO_RS14875 290 NAEGVGLKLDERGFIAVDGDCKTNLPNVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHG-HVNFNTIPWVI 360
                                            *********************************************************998.9********** PP

                              TIGR01350 347 ytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselis 418
                                            yt+Pe+a vG+te+q+k+eg+++k+g fpf ang+a+al++t+G+vk ++d kt+eilG+hivg+ aselis
  FitnessBrowser__HerbieS:HSERO_RS14875 361 YTSPEIAWVGKTEQQLKAEGVQYKAGTFPFLANGRARALGDTSGMVKFLADAKTDEILGVHIVGPMASELIS 432
                                            ************************************************************************ PP

                              TIGR01350 419 elalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                            e+++a+e+++++e++a+++h+HP+lsEa+keaala+ ++a++
  FitnessBrowser__HerbieS:HSERO_RS14875 433 EAVVAMEFRASSEDIARICHAHPSLSEATKEAALAVDKRALN 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.51
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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