Alignments for a candidate for lpd in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Saccharomonospora cyanea NA-134

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_005454631.1 SACCYDRAFT_RS06380 dihydrolipoyl dehydrogenase

Query= BRENDA::P9WHH8
         (464 letters)



>NCBI__GCF_000244975.1:WP_005454631.1
          Length = 465

 Score =  631 bits (1628), Expect = 0.0
 Identities = 311/463 (67%), Positives = 379/463 (81%), Gaps = 4/463 (0%)

Query: 3   HYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIF 62
           H+DVVVLGAGPGGY AA+RAAQLG  TA++E +YWGGVCLNVGCIPSKALLRNAEL H+F
Sbjct: 4   HFDVVVLGAGPGGYTAAVRAAQLGFDTAVIEERYWGGVCLNVGCIPSKALLRNAELAHLF 63

Query: 63  TKDAKAFGIS--GEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANT 120
           T +A+ FGI   GEVTFDY  A+ RSRKVA+GRV G+H+LMKKN IT+ +G GTF    +
Sbjct: 64  THEARTFGIKVDGEVTFDYSAAHQRSRKVADGRVKGIHYLMKKNAITQFNGRGTFTSDKS 123

Query: 121 LLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAG 180
           + V   +G  E+VTFD+ IIA G+S +L+PGTS+S  VVTYE+QIL  +LP+SI+I GAG
Sbjct: 124 IEVTTANG-VETVTFDHCIIAAGASPKLLPGTSVSDRVVTYEQQILESDLPESIVICGAG 182

Query: 181 AIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIAD 240
           AIG+EFGYVL NYGV VTIVEF+ R +P ED +VS E+ +++++LG+ +LT+T+VESI +
Sbjct: 183 AIGVEFGYVLHNYGVKVTIVEFMDRMVPAEDEEVSAELARRYRRLGIDVLTSTRVESIDE 242

Query: 241 GGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTN 300
            G +V VTV+KDG  Q L+A+KVLQA+GFAPNVEGYGL+  GVALT+R AI VD   RTN
Sbjct: 243 SGEKVRVTVSKDGEQQVLEADKVLQAMGFAPNVEGYGLENTGVALTERGAIDVDGRCRTN 302

Query: 301 VGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGL 360
           V HI+AIGDV   L LAH AE+ G+VAAETIA  ET+ L D+RM+PRAT+CQP VASFGL
Sbjct: 303 VPHIFAIGDVTAKLMLAHAAESMGIVAAETIADVETMEL-DYRMIPRATYCQPQVASFGL 361

Query: 361 TEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELL 420
           TE+QAR+EGYDV V+KFPFTAN KAHG+ D  GFVKLV+DAK+GELLGGHL+G DV ELL
Sbjct: 362 TEEQARSEGYDVQVSKFPFTANGKAHGLADAVGFVKLVSDAKYGELLGGHLIGPDVTELL 421

Query: 421 PELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMIN 463
           PELTLAQ+WDLT  E+ARNVH HPT+ EA++E  HGL GHMIN
Sbjct: 422 PELTLAQQWDLTVHEVARNVHAHPTLGEAVKEAIHGLAGHMIN 464


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: 688
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: 464
Length of database: 465
Length adjustment: 33
Effective length of query: 431
Effective length of database: 432
Effective search space:   186192
Effective search space used:   186192
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_005454631.1 SACCYDRAFT_RS06380 (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.15891.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-172  557.8   1.4     1e-171  557.6   1.4    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454631.1  SACCYDRAFT_RS06380 dihydrolipoyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454631.1  SACCYDRAFT_RS06380 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  557.6   1.4    1e-171    1e-171       1     461 []       4     465 .]       4     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 557.6 bits;  conditional E-value: 1e-171
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.akelgi 68 
                                               ++dvvv+G+GpgGY+aA+raaqlg+ +a++e++++GG+ClnvGCiP+KalL++ae+++ +++ a ++gi
  lcl|NCBI__GCF_000244975.1:WP_005454631.1   4 HFDVVVLGAGPGGYTAAVRAAQLGFDTAVIEERYWGGVCLNVGCIPSKALLRNAELAHLFTHeARTFGI 72 
                                               59******************************************************************* PP

                                 TIGR01350  69 even.vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleaknii 136
                                               +v++ v++d++++++r++kv +  v+G+++L+kkn +++++G+++++++k++ev++ ++ ++++++++i
  lcl|NCBI__GCF_000244975.1:WP_005454631.1  73 KVDGeVTFDYSAAHQRSRKVADGRVKGIHYLMKKNAITQFNGRGTFTSDKSIEVTTANGVETVTFDHCI 141
                                               ***99**************************************************************** PP

                                 TIGR01350 137 iAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldri 205
                                               iA G++p+ lp+  +++  +v+t+e+++  + +pes+vi G+G+iGvEf+++++++Gvkvt++e++dr+
  lcl|NCBI__GCF_000244975.1:WP_005454631.1 142 IAAGASPKLLPG-TSVSD-RVVTYEQQILESDLPESIVICGAGAIGVEFGYVLHNYGVKVTIVEFMDRM 208
                                               ************.55554.599999999999************************************** PP

                                 TIGR01350 206 lpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnlee 273
                                               +pa+d+evs +l++++++ g+++lt+++v+++ ++ ++v+v+ +k+ e+++lea+kvL a+G+ pn+e+
  lcl|NCBI__GCF_000244975.1:WP_005454631.1 209 VPAEDEEVSAELARRYRRLGIDVLTSTRVESIDESGEKVRVTVSKDgEQQVLEADKVLQAMGFAPNVEG 277
                                               ****************************************887777799******************** PP

                                 TIGR01350 274 lgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykav 342
                                                gle++gv l+ergai vd ++rtnvp+i+aiGDv++klmLAh A+++g+vaae+ia+ e+ e+dy+++
  lcl|NCBI__GCF_000244975.1:WP_005454631.1 278 YGLENTGVALTERGAIDVDGRCRTNVPHIFAIGDVTAKLMLAHAAESMGIVAAETIADVETMELDYRMI 346
                                               ************************************************************99******* PP

                                 TIGR01350 343 PsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivga 411
                                               P+++y++P+vas+Glteeqa++eg++v+v+kfpf+angka  l ++ Gfvk++ d k+ge+lG h++g+
  lcl|NCBI__GCF_000244975.1:WP_005454631.1 347 PRATYCQPQVASFGLTEEQARSEGYDVQVSKFPFTANGKAHGLADAVGFVKLVSDAKYGELLGGHLIGP 415
                                               ********************************************************************* PP

                                 TIGR01350 412 easeliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               +++el+ el+la +++ltv+e+a+ +h+HPtl+Ea+kea++ + g++i++
  lcl|NCBI__GCF_000244975.1:WP_005454631.1 416 DVTELLPELTLAQQWDLTVHEVARNVHAHPTLGEAVKEAIHGLAGHMINM 465
                                               **********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 9.53
//
[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