Alignments for a candidate for lpd in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudovibrio axinellae Ad2

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_068009726.1 PsAD2_RS19485 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_001623255.1:WP_068009726.1
          Length = 480

 Score =  494 bits (1273), Expect = e-144
 Identities = 254/475 (53%), Positives = 324/475 (68%), Gaps = 15/475 (3%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           +D+I++G GPGGYV AIR+AQL  K A+VER H+GGIC NWGCIPTK+LLRSA+VYH MQ
Sbjct: 6   YDVIIIGSGPGGYVTAIRSAQLGFKTAVVEREHMGGICSNWGCIPTKALLRSADVYHNMQ 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +A+ +GL++    FD   ++ RSR VA ++  GV  L++KNKV++I G   LT   ++ V
Sbjct: 66  HAKDFGLSAETIGFDAQAVVKRSRGVAGQMNGGVGYLMKKNKVDIIWGEATLTKPGEIKV 125

Query: 125 ETTEGE--------------EKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPP 170
           E  + +                   AK II+ATGAR R LP +  D   IWTY  A+ P 
Sbjct: 126 EAPKRKAYEPQAPVPKTVKGHGTYSAKHIIVATGARPRVLPGLEPDKDSIWTYFEAMVPA 185

Query: 171 AMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIR 230
            MPK L+V+GSGAIGIEFASFY   G +V++VE    I+P+ED E+SA+  K  +K+GI+
Sbjct: 186 EMPKSLVVMGSGAIGIEFASFYNTMGVDVTVVEMMSTIMPVEDPEISAHAKKQMEKQGIK 245

Query: 231 ILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDR 290
            +  + +  +      +TA I   DGK         I A+GVV NVEN+GL+ LGIK +R
Sbjct: 246 FVLDAKVSKVVKGAGQITATIETKDGKKQDITADKLISAVGVVGNVENLGLETLGIKTER 305

Query: 291 GFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGC 350
           G I  D F RTNV  ++AIGDVAG P LAHKA H+GVI  E IAG D VHP+    IPGC
Sbjct: 306 GCIVTDDFSRTNVPGIYAIGDVAGPPMLAHKAEHEGVICIEKIAGED-VHPMKRDQIPGC 364

Query: 351 TYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLG 410
           TY  PQVASVGLTE++A+  GY V++G FPF+ NGKAIA G  +G VKTVFD  +G LLG
Sbjct: 365 TYCNPQVASVGLTEQRAKDAGYEVRVGRFPFMGNGKAIALGEPEGLVKTVFDKKTGQLLG 424

Query: 411 AHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           AHMVGAEVTE+IQG+ ++  LETTE E+M T+FPHPT+SE M ESVL AYGRAL+
Sbjct: 425 AHMVGAEVTELIQGFVISMGLETTEEELMHTVFPHPTISETMKESVLDAYGRALN 479


Lambda     K      H
   0.319    0.135    0.393 

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: 653
Number of extensions: 29
Number of successful extensions: 5
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: 466
Length of database: 480
Length adjustment: 33
Effective length of query: 433
Effective length of database: 447
Effective search space:   193551
Effective search space used:   193551
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_068009726.1 PsAD2_RS19485 (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.2978816.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-177  577.1   7.5   1.4e-177  576.9   7.5    1.0  1  NCBI__GCF_001623255.1:WP_068009726.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_068009726.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.9   7.5  1.4e-177  1.4e-177       2     460 ..       6     479 ..       5     480 .] 0.98

  Alignments for each domain:
  == domain 1  score: 576.9 bits;  conditional E-value: 1.4e-177
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           ydv++iG+GpgGYv+Air+aqlg+k+a+ve+e++GG+C n+GCiPtKalL+sa+v++++++ak++g+++e++ 
  NCBI__GCF_001623255.1:WP_068009726.1   6 YDVIIIGSGPGGYVTAIRSAQLGFKTAVVEREHMGGICSNWGCIPTKALLRSADVYHNMQHAKDFGLSAETIG 78 
                                           9************************************************************************ PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...............kklea 132
                                           +d +++++r++ v  +++gGv +L+kknkv+ i+Gea+l++++e++v++ k++                +++a
  NCBI__GCF_001623255.1:WP_068009726.1  79 FDAQAVVKRSRGVAGQMNGGVGYLMKKNKVDIIWGEATLTKPGEIKVEAPKRKayepqapvpktvkghGTYSA 151
                                           ***********************************************99887788999****8877766778* PP

                             TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldri 205
                                           k+ii+AtG++pr lp+ le d++ ++t+ ea+   e+p+slv++G+G+iG+Efas+++++Gv+vtv+e++++i
  NCBI__GCF_001623255.1:WP_068009726.1 152 KHIIVATGARPRVLPG-LEPDKDSIWTYFEAMVPAEMPKSLVVMGSGAIGIEFASFYNTMGVDVTVVEMMSTI 223
                                           ****************.******************************************************** PP

                             TIGR01350 206 lpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgl 276
                                           +p++d e+s  +kk+++k+g+k++ +akv++v k + +++  +e+k+++++ ++a+k++ avG+  n+e+lgl
  NCBI__GCF_001623255.1:WP_068009726.1 224 MPVEDPEISAHAKKQMEKQGIKFVLDAKVSKVVKGAGQITatIETKDGKKQDITADKLISAVGVVGNVENLGL 296
                                           ***************************************97778888899*********************** PP

                             TIGR01350 277 eklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviyte 349
                                           e+lg+++ erg+i++d+  rtnvpgiyaiGDv+g++mLAh+A++egv+++ekiag+  + ++++++P ++y++
  NCBI__GCF_001623255.1:WP_068009726.1 297 ETLGIKT-ERGCIVTDDFSRTNVPGIYAIGDVAGPPMLAHKAEHEGVICIEKIAGEDVHPMKRDQIPGCTYCN 368
                                           ******5.56**********************************************999************** PP

                             TIGR01350 350 PevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselal 422
                                           P+vasvGlte+ ak++g+ev+vg+fpf+ ngka+al+e +G+vk+++dkktg++lGah+vgae++eli+ +++
  NCBI__GCF_001623255.1:WP_068009726.1 369 PQVASVGLTEQRAKDAGYEVRVGRFPFMGNGKAIALGEPEGLVKTVFDKKTGQLLGAHMVGAEVTELIQGFVI 441
                                           ************************************************************************* PP

                             TIGR01350 423 aveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                            + le+t+eel++t++pHPt+sE++ke++l+a+g+a++
  NCBI__GCF_001623255.1:WP_068009726.1 442 SMGLETTEEELMHTVFPHPTISETMKESVLDAYGRALN 479
                                           *********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (480 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: 00:00:00.00
# Mc/sec: 22.36
//
[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 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