Alignments for a candidate for lpd in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Derxia gummosa DSM 723

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_028313012.1 H566_RS0121210 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_000482785.1:WP_028313012.1
          Length = 475

 Score =  499 bits (1284), Expect = e-145
 Identities = 264/476 (55%), Positives = 331/476 (69%), Gaps = 7/476 (1%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           M+Q+FDVVVIGAGPGGYVAAIRAAQLGLK AC++ +    G  A GGTC NVGCIPSKAL
Sbjct: 1   MAQQFDVVVIGAGPGGYVAAIRAAQLGLKVACVDAWKNARGGPAPGGTCTNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           L SS  +  A   F  HGI    +++DVP M+ARK  +V     GI  LF+ N VT F G
Sbjct: 61  LQSSEHFEHAAHGFAEHGISLDNLSMDVPKMIARKDAVVDQNNQGILFLFRKNKVTFFHG 120

Query: 121 HGKLLAN----KQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALE 176
               +       +++VTG   K + L A+NVI+A+GS    +P A   ++ ++ + GAL 
Sbjct: 121 LASFVKTGAEGTEIKVTG--AKEEDLIAKNVIVATGSNARALPLAAFDEEKVLSNDGALR 178

Query: 177 FQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQG 236
             AVP KLG+IGAGVIGLE+GSVW RLGA+VTVLE L  FL A DE++AKEA K LTKQG
Sbjct: 179 VGAVPAKLGIIGAGVIGLEMGSVWRRLGADVTVLEGLPNFLAAVDEEVAKEAHKQLTKQG 238

Query: 237 LNIRLGARVTASEVKKKQVTVTFTDANGE-QKETFDKLIVAVGRRPVTTDLLAADSGVTL 295
           L I LG +++  +   + VT+ + +A GE Q    DKLIV++GR   T  L     G+ L
Sbjct: 239 LKIELGVQISEVKTDGEGVTIAYANAKGEAQTLAVDKLIVSIGRVANTNGLNGEAVGLPL 298

Query: 296 DERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPS 355
           DERGFI VD+ CKTSVPG++A+GDVVRG MLAHKA EEGV VAERIAG    +N++ IP 
Sbjct: 299 DERGFIVVDEDCKTSVPGIWAVGDVVRGPMLAHKAEEEGVAVAERIAGKHGHVNFNTIPW 358

Query: 356 VIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVL 415
           VIYT PEIAWVGKTEQ LK EGV+   G FPF A+GRA A  DTTG VK +ADA+TD +L
Sbjct: 359 VIYTSPEIAWVGKTEQQLKTEGVKYKAGKFPFLANGRARALGDTTGFVKFLADAETDEIL 418

Query: 416 GVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           GVH+IGP  +EL+ +G + MEF  S+ED+GM+  +HP+LSE+  EAALAV G  ++
Sbjct: 419 GVHMIGPMVSELISEGVVAMEFKASSEDIGMICHAHPSLSESTKEAALAVLGRTLN 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: 719
Number of extensions: 27
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: 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 WP_028313012.1 H566_RS0121210 (dihydrolipoyl 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.28802.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-166  539.8   4.9   2.9e-166  539.6   4.9    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028313012.1  H566_RS0121210 dihydrolipoyl deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028313012.1  H566_RS0121210 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.6   4.9  2.9e-166  2.9e-166       1     460 [.       4     474 ..       4     475 .] 0.96

  Alignments for each domain:
  == domain 1  score: 539.6 bits;  conditional E-value: 2.9e-166
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.ek......lGGtClnvGCiPtKalLksaevveelke 62 
                                               ++dvvviG+GpgGYvaAiraaqlglkva+v+  ++       GGtC+nvGCiP+KalL+s+e +e++ +
  lcl|NCBI__GCF_000482785.1:WP_028313012.1   4 QFDVVVIGAGPGGYVAAIRAAQLGLKVACVDAwKNarggpaPGGTCTNVGCIPSKALLQSSEHFEHAAH 72 
                                               59****************************9753322233269************************** PP

                                 TIGR01350  63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld....kkevevkkekk 126
                                                ++e+gi+++n+++d+ k+ +rk++vv++ ++G+ +L++knkv+ ++G a++++     +e++v++ k 
  lcl|NCBI__GCF_000482785.1:WP_028313012.1  73 gFAEHGISLDNLSMDVPKMIARKDAVVDQNNQGILFLFRKNKVTFFHGLASFVKtgaeGTEIKVTGAK- 140
                                               ****************************************************996665679****998. PP

                                 TIGR01350 127 ekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvk 195
                                               e+ l akn+i+AtGs+ r+lpl  ++de+ v+++++al++  vp +l i+G+GviG+E++s++++lG++
  lcl|NCBI__GCF_000482785.1:WP_028313012.1 141 EEDLIAKNVIVATGSNARALPL-AAFDEEKVLSNDGALRVGAVPAKLGIIGAGVIGLEMGSVWRRLGAD 208
                                               56999*****************.8888888*************************************** PP

                                 TIGR01350 196 vtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvL 262
                                               vtv+e l++ l+a+d+ev+k+++k+l+k+g+ki  + +++ev+++ + v+  + + k+e++tl ++k++
  lcl|NCBI__GCF_000482785.1:WP_028313012.1 209 VTVLEGLPNFLAAVDEEVAKEAHKQLTKQGLKIELGVQISEVKTDGEGVTiaYANAKGEAQTLAVDKLI 277
                                               ************************************************99766666679********** PP

                                 TIGR01350 263 vavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiag 331
                                               v++Gr +n+++l+ e++g+ lderg+i+vde+++t+vpgi+a+GDv++++mLAh+A++egv +ae+iag
  lcl|NCBI__GCF_000482785.1:WP_028313012.1 278 VSIGRVANTNGLNGEAVGLPLDERGFIVVDEDCKTSVPGIWAVGDVVRGPMLAHKAEEEGVAVAERIAG 346
                                               ********************************************************************* PP

                                 TIGR01350 332 kekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkkt 400
                                               k+  +++ +++P viyt+Pe+a vG+te+q+k eg+++k+gkfpf ang+a+al++t+Gfvk ++d +t
  lcl|NCBI__GCF_000482785.1:WP_028313012.1 347 KHG-HVNFNTIPWVIYTSPEIAWVGKTEQQLKTEGVKYKAGKFPFLANGRARALGDTTGFVKFLADAET 414
                                               998.9**************************************************************** PP

                                 TIGR01350 401 geilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               +eilG+h++g+ +selise ++a+e+++++e++ +++h+HP+lsE +keaala+lg++++
  lcl|NCBI__GCF_000482785.1:WP_028313012.1 415 DEILGVHMIGPMVSELISEGVVAMEFKASSEDIGMICHAHPSLSESTKEAALAVLGRTLN 474
                                               ******************************************************998876 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.78
//
[ok]

This GapMind analysis is from Sep 24 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