Alignments for a candidate for lpd in Frankia alni ACN14a

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Frankia alni ACN14a

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_041940589.1 FRAAL_RS15765 dihydrolipoyl dehydrogenase

Query= BRENDA::P9WHH8
         (464 letters)



>NCBI__GCF_000058485.1:WP_041940589.1
          Length = 467

 Score =  653 bits (1684), Expect = 0.0
 Identities = 329/465 (70%), Positives = 382/465 (82%), Gaps = 4/465 (0%)

Query: 3   HYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIF 62
           H+DVVVLGAGPGGYVAAIRAAQLGL+TA+VE +YWGGVCLNVGCIPSKALLRNAELVH  
Sbjct: 4   HFDVVVLGAGPGGYVAAIRAAQLGLTTAVVEERYWGGVCLNVGCIPSKALLRNAELVHTL 63

Query: 63  TKDAKAFGIS--GEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANT 120
           T +AK FGIS  G +T DYG A+ RSRKVA+GRV GVHFLMKKN ITE  G GTF D +T
Sbjct: 64  THEAKTFGISVDGSITVDYGAAFQRSRKVADGRVKGVHFLMKKNNITEYSGRGTFVDDHT 123

Query: 121 LLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAG 180
           L V   DG T +VTFD+ IIA G++ RL+PGTSLS  VVTYE+QILS ELP+SI+IAGAG
Sbjct: 124 LSVTGADGATSTVTFDHVIIAAGATPRLLPGTSLSERVVTYEQQILSSELPRSIVIAGAG 183

Query: 181 AIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIAD 240
           AIG+EFGYVL+NYGVDVTIVEFL R +P EDA+VS E+ K +KK G+TILT+T+V+SI D
Sbjct: 184 AIGVEFGYVLRNYGVDVTIVEFLDRVVPLEDAEVSAELAKHYKKAGITILTSTRVDSIDD 243

Query: 241 GGSQVTVTVT-KDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRT 299
            G  V VTVT  DGV++ L+ EKVLQAIGF PNV GYGL+  GVALT+R AI VD Y RT
Sbjct: 244 SGDTVKVTVTGSDGVSKVLETEKVLQAIGFGPNVTGYGLENTGVALTERGAIDVDGYCRT 303

Query: 300 NVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFG 359
           NV HI+AIGDV   L LAH AEA G++AAETI  AET  L D+ M+PRAT+CQP VASFG
Sbjct: 304 NVPHIFAIGDVTAKLMLAHAAEAMGIIAAETIGDAETYPL-DYVMIPRATYCQPQVASFG 362

Query: 360 LTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAEL 419
            TE QAR+ GYDV VAKFPF+AN KAHG+G+ +GFVK+++DAK+GELLG HL+G DV EL
Sbjct: 363 YTEAQARDAGYDVKVAKFPFSANGKAHGLGETAGFVKILSDAKYGELLGAHLIGPDVTEL 422

Query: 420 LPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
           LPELTLAQRWDLT +ELARNVH HPT+ E+++E  HGL GHMINF
Sbjct: 423 LPELTLAQRWDLTVAELARNVHAHPTLGESVKEALHGLAGHMINF 467


Lambda     K      H
   0.318    0.136    0.390 

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: 733
Number of extensions: 22
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: 464
Length of database: 467
Length adjustment: 33
Effective length of query: 431
Effective length of database: 434
Effective search space:   187054
Effective search space used:   187054
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_041940589.1 FRAAL_RS15765 (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.1377263.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-172  559.6   0.8   2.9e-172  559.4   0.8    1.0  1  NCBI__GCF_000058485.1:WP_041940589.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000058485.1:WP_041940589.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.4   0.8  2.9e-172  2.9e-172       1     460 [.       4     466 ..       4     467 .] 0.97

  Alignments for each domain:
  == domain 1  score: 559.4 bits;  conditional E-value: 2.9e-172
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 
                                           ++dvvv+G+GpgGYvaAiraaqlgl +a+ve++++GG+ClnvGCiP+KalL++ae+v++l++ ak++gi+v++
  NCBI__GCF_000058485.1:WP_041940589.1   4 HFDVVVLGAGPGGYVAAIRAAQLGLTTAVVEERYWGGVCLNVGCIPSKALLRNAELVHTLTHeAKTFGISVDG 76 
                                           59**********************************************************************9 PP

                             TIGR01350  73 .vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                            +++d+ ++ +r++kv +  v+Gv++L+kkn++++++G+++++d+++++v++ +++ ++++++++iiA G++p
  NCBI__GCF_000058485.1:WP_041940589.1  77 sITVDYGAAFQRSRKVADGRVKGVHFLMKKNNITEYSGRGTFVDDHTLSVTGADGAtSTVTFDHVIIAAGATP 149
                                           9***************************************************9988799************** PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                           r lp+  + +e +v+t+e+++  +e+p+s+vi G+G+iGvEf+++++++Gv+vt++e+ldr++p +daevs +
  NCBI__GCF_000058485.1:WP_041940589.1 150 RLLPG-TSLSE-RVVTYEQQILSSELPRSIVIAGAGAIGVEFGYVLRNYGVDVTIVEFLDRVVPLEDAEVSAE 220
                                           *****.55555.69999999999************************************************** PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           l+k++kk g++ilt+++v ++ ++ d+v+v+  ++    ++le+ekvL a+G+ pn+++ gle++gv l+erg
  NCBI__GCF_000058485.1:WP_041940589.1 221 LAKHYKKAGITILTSTRVDSIDDSGDTVKVTVTGSdgVSKVLETEKVLQAIGFGPNVTGYGLENTGVALTERG 293
                                           ***************************997776664357899******************************* PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           ai vd ++rtnvp+i+aiGDv++klmLAh A+++g++aae+i ++e+  +dy ++P+++y++P+vas+G+te+
  NCBI__GCF_000058485.1:WP_041940589.1 294 AIDVDGYCRTNVPHIFAIGDVTAKLMLAHAAEAMGIIAAETIGDAETYPLDYVMIPRATYCQPQVASFGYTEA 366
                                           ********************************************9999************************* PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           qa+++g++vkv+kfpf+angka  l+et Gfvk++ d k+ge+lGah++g++++el+ el+la +++ltv el
  NCBI__GCF_000058485.1:WP_041940589.1 367 QARDAGYDVKVAKFPFSANGKAHGLGETAGFVKILSDAKYGELLGAHLIGPDVTELLPELTLAQRWDLTVAEL 439
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgkaih 460
                                           a+ +h+HPtl+E +kea++ + g++i+
  NCBI__GCF_000058485.1:WP_041940589.1 440 ARNVHAHPTLGESVKEALHGLAGHMIN 466
                                           **********************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (467 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: 29.57
//
[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