Alignments for a candidate for lpd in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Hyphomicrobium sulfonivorans WDL6

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_068459706.1 APY04_RS03445 dihydrolipoyl dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>NCBI__GCF_001541235.1:WP_068459706.1
          Length = 466

 Score =  535 bits (1378), Expect = e-156
 Identities = 270/463 (58%), Positives = 340/463 (73%), Gaps = 1/463 (0%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+++IG GPGGYV AI+A+QLG+K   +EKR   GGTCLNVGCIPSKALLH+S +Y EA 
Sbjct: 5   DLIVIGAGPGGYVCAIRASQLGMKVAIVEKRPRFGGTCLNVGCIPSKALLHASELYDEAG 64

Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164
           H FA+ G++V   +++L  MLA KD AVK  T GV  L +KNK+++  G G+ L    V 
Sbjct: 65  HAFADMGIEVKP-KLNLAQMLAFKDDAVKGNTEGVAYLMRKNKIDHFHGTGRILGAGRVE 123

Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLTEIPKKLIVIGAGY 224
           V  I+GE   V    I++ATGSDV  LPGI IDEK IVSSTGALSL ++PK+L+VIGAG 
Sbjct: 124 VTFINGEQQEVDATSIVIATGSDVAQLPGIEIDEKAIVSSTGALSLEKVPKRLVVIGAGV 183

Query: 225 IGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVDSS 284
           IGLE+GSVW RLGSEVTVVE+   I+P  D E+ KQ QR LEKQ M F L  KV GV  +
Sbjct: 184 IGLELGSVWRRLGSEVTVVEYLDRILPGNDLEVAKQLQRLLEKQGMAFRLGHKVTGVKKN 243

Query: 285 GDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERFST 344
           G    + +EPA GG+  TL ADVVLV+ GR P+T GL L + GV+ DK GR+ V+  + +
Sbjct: 244 GAAQAVSIEPAAGGDADTLAADVVLVAIGRVPYTRGLGLSEAGVQLDKRGRVEVDAHYQS 303

Query: 345 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVGKT 404
           NV G+YAIGDVI GPMLAHKAE++GVA  E +AG+ GHV+Y  +P VVYT PEVASVGK+
Sbjct: 304 NVPGIYAIGDVIKGPMLAHKAEDEGVALAELLAGQAGHVNYGIIPAVVYTSPEVASVGKS 363

Query: 405 EEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGELIH 464
           EE+LK EGV+YNVGKFPF AN RAKA    +G VK+LAD  TD++LGVH++  NA E+I 
Sbjct: 364 EEELKAEGVAYNVGKFPFTANGRAKANKQTDGFVKVLADAATDRVLGVHMVGANASEIIA 423

Query: 465 EAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507
           EA + + +  S+ED+AR CHAHPT++EA+KEAA+A   + IHM
Sbjct: 424 EAAVLMEFGGSAEDLARTCHAHPTLTEAVKEAALAVEKRAIHM 466


Lambda     K      H
   0.315    0.134    0.376 

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: 667
Number of extensions: 30
Number of successful extensions: 3
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: 507
Length of database: 466
Length adjustment: 34
Effective length of query: 473
Effective length of database: 432
Effective search space:   204336
Effective search space used:   204336
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: 52 (24.6 bits)

Align candidate WP_068459706.1 APY04_RS03445 (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.1243713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-177  576.8   8.9   1.7e-177  576.7   8.9    1.0  1  NCBI__GCF_001541235.1:WP_068459706.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001541235.1:WP_068459706.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.7   8.9  1.7e-177  1.7e-177       2     461 .]       4     466 .]       3     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 576.7 bits;  conditional E-value: 1.7e-177
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 
                                           yd++viG+GpgGYv+Aira+qlg+kva+vek  ++GGtClnvGCiP+KalL+++e+++e+ + ++++giev +
  NCBI__GCF_001541235.1:WP_068459706.1   4 YDLIVIGAGPGGYVCAIRASQLGMKVAIVEKrPRFGGTCLNVGCIPSKALLHASELYDEAGHaFADMGIEV-K 75 
                                           9******************************899***********************************98.7 PP

                             TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepr 144
                                            kl+l+++l+ k+  vk  ++Gv++L++knk+++++G++++l++++vev+  ++e ++++a +i+iAtGs+++
  NCBI__GCF_001541235.1:WP_068459706.1  76 PKLNLAQMLAFKDDAVKGNTEGVAYLMRKNKIDHFHGTGRILGAGRVEVTFINGEqQEVDATSIVIATGSDVA 148
                                           9*************************************************98877689*************** PP

                             TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvl 217
                                           +lp+ +e dek +++s++al+l++vp++lv++G+GviG+E++s++++lG++vtv+e+ldrilp +d ev+k+l
  NCBI__GCF_001541235.1:WP_068459706.1 149 QLPG-IEIDEKAIVSSTGALSLEKVPKRLVVIGAGVIGLELGSVWRRLGSEVTVVEYLDRILPGNDLEVAKQL 220
                                           ****.******************************************************************** PP

                             TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           ++ l+k+g+ +  ++kvt v+k+ ++    +e   + +++tl a+ vLva+Gr p +++lgl + gv+ld+rg
  NCBI__GCF_001541235.1:WP_068459706.1 221 QRLLEKQGMAFRLGHKVTGVKKNGAAQAvsIEPAAGgDADTLAADVVLVAIGRVPYTRGLGLSEAGVQLDKRG 293
                                           ******************888876654423666555699********************************** PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           +++vd++++ nvpgiyaiGDvi+++mLAh+A++egv  ae +ag++  +++y  +P+v+yt+PevasvG++ee
  NCBI__GCF_001541235.1:WP_068459706.1 294 RVEVDAHYQSNVPGIYAIGDVIKGPMLAHKAEDEGVALAELLAGQAG-HVNYGIIPAVVYTSPEVASVGKSEE 365
                                           ********************************************998.9************************ PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           ++k+eg++++vgkfpf+ang+a a ++tdGfvkv++d  t+++lG+h+vga+ase+i+e+a+++e+++++e+l
  NCBI__GCF_001541235.1:WP_068459706.1 366 ELKAEGVAYNVGKFPFTANGRAKANKQTDGFVKVLADAATDRVLGVHMVGANASEIIAEAAVLMEFGGSAEDL 438
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgkaihv 461
                                           a+t+h+HPtl+Ea+keaala+ ++aih+
  NCBI__GCF_001541235.1:WP_068459706.1 439 ARTCHAHPTLTEAVKEAALAVEKRAIHM 466
                                           ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.12
//
[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