Alignments for a candidate for lpd in Novosphingobium fuchskuhlense FNE08-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Novosphingobium fuchskuhlense FNE08-7

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_067911249.1 AQZ52_RS12610 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_001519075.1:WP_067911249.1
          Length = 470

 Score =  582 bits (1501), Expect = e-171
 Identities = 293/470 (62%), Positives = 358/470 (76%), Gaps = 6/470 (1%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MAD +DL+VLG GPGGYVAAIR AQL LKV +VER  LGGICLNWGCIPTK+LLRSAEV+
Sbjct: 1   MADQYDLLVLGSGPGGYVAAIRGAQLGLKVGIVERELLGGICLNWGCIPTKALLRSAEVF 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
           ++M++A +YGL +     D+D ++ RSR VA +L  GV  L+RKNK+ V  G G + G  
Sbjct: 61  NQMKHAASYGLAADNIRADIDAVVKRSRGVAKQLNQGVTHLMRKNKITVHMGTGVIKGAG 120

Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180
           Q+ V   +G E +L AK +I+ATGARAR LP   +DG  IWTY HA+ PPAMP KLLVIG
Sbjct: 121 QVEVTGEKGTE-VLSAKHVIVATGARARDLPFAKADGDRIWTYRHAMVPPAMPTKLLVIG 179

Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240
           SGAIGIEFASFY D GA+V++VE   +I+P+EDA+VSA++ K+  K+GI ILT + ++++
Sbjct: 180 SGAIGIEFASFYNDMGADVTVVEMMDRIVPVEDADVSAFLEKSLTKQGITILTGAGVESI 239

Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGR 300
                GV A+I G DG   +  FSH IVA+G+V N ENIGL+ LG+  +RG IA+DG+GR
Sbjct: 240 ATSAAGVKAKIKGKDGNSAEHDFSHVIVAVGIVPNTENIGLEALGVAAERGIIAIDGYGR 299

Query: 301 TNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGC-----DHVHPLNTQNIPGCTYARP 355
           TNV  VWAIGDV   P LAHKASH+GVIAAEAIA        H HP++  NIPGCTY  P
Sbjct: 300 TNVPGVWAIGDVTPGPWLAHKASHEGVIAAEAIAQALGNTEVHPHPMDRLNIPGCTYCHP 359

Query: 356 QVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVG 415
           QVASVGLTE KA++ G+ VK+G FPFI NGKAIA G  +GF+KTVFDA +G LLGAHM+G
Sbjct: 360 QVASVGLTEAKAKEAGHEVKVGTFPFIGNGKAIALGEAEGFIKTVFDAQTGELLGAHMIG 419

Query: 416 AEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           AEVTE+IQGY V +TLETTEAE+M T+F HPTLSE MHESVLAAYGRALH
Sbjct: 420 AEVTELIQGYVVGKTLETTEAELMHTVFAHPTLSEMMHESVLAAYGRALH 469


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: 768
Number of extensions: 26
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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_067911249.1 AQZ52_RS12610 (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.1292577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-171  556.5   9.7   2.5e-171  556.3   9.7    1.0  1  NCBI__GCF_001519075.1:WP_067911249.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001519075.1:WP_067911249.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.3   9.7  2.5e-171  2.5e-171       1     461 []       4     470 .]       4     470 .] 0.97

  Alignments for each domain:
  == domain 1  score: 556.3 bits;  conditional E-value: 2.5e-171
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           +yd++v+G+GpgGYvaAir aqlglkv +ve+e lGG+Cln+GCiPtKalL+saev++++k+a+++g+ ++n+
  NCBI__GCF_001519075.1:WP_067911249.1   4 QYDLLVLGSGPGGYVAAIRGAQLGLKVGIVERELLGGICLNWGCIPTKALLRSAEVFNQMKHAASYGLAADNI 76 
                                           69*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146
                                           + d++++++r++ v k+l++Gv++L++knk++v++G++ ++++++vev++ek++++l+ak++i+AtG++ r l
  NCBI__GCF_001519075.1:WP_067911249.1  77 RADIDAVVKRSRGVAKQLNQGVTHLMRKNKITVHMGTGVIKGAGQVEVTGEKGTEVLSAKHVIVATGARARDL 149
                                           ************************************************************************* PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           p+  ++d+++++t+++a+  + +p++l+++G+G+iG+Efas+++++G++vtv+e++dri+p++da+vs +l+k
  NCBI__GCF_001519075.1:WP_067911249.1 150 PF-AKADGDRIWTYRHAMVPPAMPTKLLVIGSGAIGIEFASFYNDMGADVTVVEMMDRIVPVEDADVSAFLEK 221
                                           **.9999999*************************************************************** PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaik 290
                                           +l+k+g++ilt+a v+++ ++++ v++++k+k  +  + +  +v+vavG  pn+e++gle+lgv  + rg+i 
  NCBI__GCF_001519075.1:WP_067911249.1 222 SLTKQGITILTGAGVESIATSAAGVKAKIKGKdgNSAEHDFSHVIVAVGIVPNTENIGLEALGVAAE-RGIIA 293
                                           **************************88887743566677789*********************965.5**** PP

                             TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks......eidykavPsviytePevasvGl 357
                                           +d + rtnvpg++aiGDv+ ++ LAh+As+egv+aae+ia++  +       +d+  +P ++y++P+vasvGl
  NCBI__GCF_001519075.1:WP_067911249.1 294 IDGYGRTNVPGVWAIGDVTPGPWLAHKASHEGVIAAEAIAQALGNtevhphPMDRLNIPGCTYCHPQVASVGL 366
                                           ***************************************9766555668889********************* PP

                             TIGR01350 358 teeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltv 430
                                           te++ake+g+evkvg fpf  ngka+al+e++Gf+k+++d +tge+lGah++gae++eli+  ++  +le+t+
  NCBI__GCF_001519075.1:WP_067911249.1 367 TEAKAKEAGHEVKVGTFPFIGNGKAIALGEAEGFIKTVFDAQTGELLGAHMIGAEVTELIQGYVVGKTLETTE 439
                                           ************************************************************************* PP

                             TIGR01350 431 eelaktihpHPtlsEaikeaalaalgkaihv 461
                                            el++t+++HPtlsE+++e++laa+g+a+h+
  NCBI__GCF_001519075.1:WP_067911249.1 440 AELMHTVFAHPTLSEMMHESVLAAYGRALHI 470
                                           ***************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (470 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.41
//
[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