GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Algoriphagus aquaeductus T4

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_111392326.1 CLV31_RS07900 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_003253485.1:WP_111392326.1
          Length = 465

 Score =  444 bits (1141), Expect = e-129
 Identities = 230/461 (49%), Positives = 316/461 (68%), Gaps = 2/461 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FDLIVLG GPGGYVAAIRA+QL LK A+VE   LGGICLNWGCIPTK+LL+SA+V+  + 
Sbjct: 6   FDLIVLGSGPGGYVAAIRASQLGLKTAIVEAAELGGICLNWGCIPTKALLKSAQVFEYIS 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +A+ YG++    + D   ++ RSR VA  ++ GV+ L++KNK+E+I+G G++   +++ V
Sbjct: 66  HAKDYGISVQGAEADFAGMVKRSRGVADGMSKGVQFLMKKNKIEIITGWGKVQPGKKVEV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
              EG++ ++ A +IIIATGAR+R+LP++  D K I  Y  A+     PKK++V+GSGAI
Sbjct: 126 NDAEGKKSVITADNIIIATGARSRELPSMKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAI 185

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           G+EFA FY   G EV+IVE   +I+P+ED EVS  + K +KK G++I+T S +  +    
Sbjct: 186 GVEFAYFYNSIGTEVTIVEFMDRIVPVEDEEVSKALEKIYKKSGMKIMTSSEVTGVDTKG 245

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
           EG    +  A G+   E     + A GVV+N+ENIGL+ +GI +D+G I V+ + +TN+ 
Sbjct: 246 EGCKVTVKTAKGEEILE-CDVVLSAAGVVSNLENIGLEDVGILVDKGKIQVNEYYQTNMP 304

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
             +AIGDV   P LAH AS +G+I  E IAG  H   L+  NIPGCTY  P++ASVG+TE
Sbjct: 305 GYYAIGDVVPGPALAHVASAEGIICVEKIAG-HHPEALDYGNIPGCTYCSPEIASVGMTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
            KA+  G+ V++G FPF A+GKA A GA DGFVK VFD   G LLGAHM+GA VTEMI  
Sbjct: 364 AKAKAAGHEVRVGKFPFSASGKASAAGAKDGFVKLVFDKKYGELLGAHMIGANVTEMIAE 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
               R LETT  E+++T+ PHPT+SEA+ E+  AAY   +H
Sbjct: 424 IVAIRKLETTGHELIKTVHPHPTMSEAIMEAAAAAYDEVIH 464


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: 592
Number of extensions: 24
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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_111392326.1 CLV31_RS07900 (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.2831899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-176  572.2  17.2   4.5e-176  572.0  17.2    1.0  1  NCBI__GCF_003253485.1:WP_111392326.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003253485.1:WP_111392326.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.0  17.2  4.5e-176  4.5e-176       1     460 [.       5     464 ..       5     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: 572.0 bits;  conditional E-value: 4.5e-176
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           ++d++v+G+GpgGYvaAira+qlglk+a+ve  +lGG+Cln+GCiPtKalLksa+v+e++++ak++gi+v++ 
  NCBI__GCF_003253485.1:WP_111392326.1   5 KFDLIVLGSGPGGYVAAIRASQLGLKTAIVEAAELGGICLNWGCIPTKALLKSAQVFEYISHAKDYGISVQGA 77 
                                           59*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepre 145
                                           + d++ +++r++ v + +++Gv++L+kknk+e i+G +k++  k+vev++ +++ ++++a+niiiAtG++ re
  NCBI__GCF_003253485.1:WP_111392326.1  78 EADFAGMVKRSRGVADGMSKGVQFLMKKNKIEIITGWGKVQPGKKVEVNDAEGKkSVITADNIIIATGARSRE 150
                                           *************************************************9998867899************** PP

                             TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218
                                           lp  ++ d k +i +++a++l+++p+++v+vG+G+iGvEfa++++++G++vt++e++dri+p++d+evsk+l+
  NCBI__GCF_003253485.1:WP_111392326.1 151 LPS-MKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAIGVEFAYFYNSIGTEVTIVEFMDRIVPVEDEEVSKALE 222
                                           ***.9******************************************************************** PP

                             TIGR01350 219 kklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergai 289
                                           k +kk+g+ki+t+++vt v ++ +  +  v++ k+ +e le + vL a G+ +nle++gle +g+ +d+ g+i
  NCBI__GCF_003253485.1:WP_111392326.1 223 KIYKKSGMKIMTSSEVTGVDTKGEGCKvtVKTAKG-EEILECDVVLSAAGVVSNLENIGLEDVGILVDK-GKI 293
                                           *****************887777766621555555.69******************************9.99* PP

                             TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqa 362
                                           +v+e+++tn+pg yaiGDv+ ++ LAhvAs+eg++++ekiag++++++dy  +P ++y++Pe+asvG+te++a
  NCBI__GCF_003253485.1:WP_111392326.1 294 QVNEYYQTNMPGYYAIGDVVPGPALAHVASAEGIICVEKIAGHHPEALDYGNIPGCTYCSPEIASVGMTEAKA 366
                                           ************************************************************************* PP

                             TIGR01350 363 keegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelak 435
                                           k++g+ev+vgkfpf+a+gka a++ +dGfvk+++dkk+ge+lGah++ga+++e+i+e++++ +le+t +el k
  NCBI__GCF_003253485.1:WP_111392326.1 367 KAAGHEVRVGKFPFSASGKASAAGAKDGFVKLVFDKKYGELLGAHMIGANVTEMIAEIVAIRKLETTGHELIK 439
                                           ************************************************************************* PP

                             TIGR01350 436 tihpHPtlsEaikeaalaalgkaih 460
                                           t+hpHPt+sEai+eaa+aa+++ ih
  NCBI__GCF_003253485.1:WP_111392326.1 440 TVHPHPTMSEAIMEAAAAAYDEVIH 464
                                           **********************999 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: 00:00:00.01
# Mc/sec: 17.01
//
[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:

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:

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:

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:

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