GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Haloterrigena daqingensis JX313

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_076582962.1 BB347_RS13020 dihydrolipoyl dehydrogenase

Query= BRENDA::Q04829
         (475 letters)



>NCBI__GCF_001971705.1:WP_076582962.1
          Length = 487

 Score =  634 bits (1634), Expect = 0.0
 Identities = 323/488 (66%), Positives = 376/488 (77%), Gaps = 14/488 (2%)

Query: 1   MVVGDIATGTELLVIGAGPGGYVAAIRAAQNGIDTTLVEKDAYGGTCLNYGCIPSKALIT 60
           MVVGD+ T T++LVIGAGP GYVAAIRA Q  +D TLVEK+AYGGTCLN+GCIPSKALIT
Sbjct: 1   MVVGDVTTATDVLVIGAGPAGYVAAIRAGQLDLDVTLVEKEAYGGTCLNHGCIPSKALIT 60

Query: 61  GANLAHEAGNAEEMGIHADPVVDMSQLRDWKSGVVDQLTGGVEKLCKANGVNLVEGTARF 120
             ++AH A  AEEMGIHADP +D+S +  WK GVVDQLT GVEKLCKAN V+L+EGTA F
Sbjct: 61  ATDVAHGAATAEEMGIHADPAIDLSGMVSWKDGVVDQLTSGVEKLCKANQVSLLEGTATF 120

Query: 121 KDENAVRIAHGGEGQGSETIEFEHCIIATGSRVIQIPGFDFGDEPVWSSRDALEADTVPE 180
            DE+  RI+H GEGQGSE++EFEH I+ATGSR I IP F F  +PV  SR AL  D+VP+
Sbjct: 121 VDEHTARISHSGEGQGSESLEFEHAIVATGSRPIAIPDFSFDADPVIDSRQALALDSVPD 180

Query: 181 RLVVVGGGYIGMELSTTFAKLGADVTVVEMLDDILPGYESDVARVVRKRAEELGIDMHLG 240
            LVVVG GYIGMEL++ +AKLG DVTVVEMLD ILPGY+ D+ R V++RA +LGI+    
Sbjct: 181 SLVVVGAGYIGMELASVYAKLGTDVTVVEMLDSILPGYDDDLKRPVKQRANDLGIEFVFE 240

Query: 241 EGASGWREEDDGIMVTTETEDG-------------EENEYRADKVLVAVGRSPVTDTMDI 287
             AS W E D+ I V  E  DG             E  E   +KVLVAVGR PV+DT+D+
Sbjct: 241 HTASEWYEPDEDIRVVAEPVDGAAANGGSAEAIDEERLELDVEKVLVAVGREPVSDTLDL 300

Query: 288 ENAGLEADDRGFLSVDDRRRTDVEHIYAVGDVVEDTPMLAHVASKEGIVAAEHVAGEPVA 347
           E AG+E DDRG +  D R RT+V+HI+AVGDV  + PMLAH  S EG  AAE +AGEP A
Sbjct: 301 EAAGVETDDRGIIQTDTRARTNVDHIFAVGDVAGE-PMLAHKGSMEGQTAAEVIAGEPAA 359

Query: 348 FDSQAVPAAVFTDPEIGTVGMTEADAEEAGFTPVVGQMPFRASGRALTTNHADGFVRVVA 407
            D QA+PA VFTDPEI TVG+TE DAEEAG+ PVVGQ PFRASGRALTT  ADGFV++VA
Sbjct: 360 IDHQAMPAVVFTDPEIATVGLTETDAEEAGYDPVVGQFPFRASGRALTTGDADGFVKIVA 419

Query: 408 DEESGFVLGAQIVGPEASELIAELAFAIEMGATLEDVASTIHTHPTLAEAVMEAAENALG 467
           +E  G+VLGA IVGPEASELIAEL  AIE+GATLEDVAST+H HPTL+E+VMEAAENALG
Sbjct: 420 EESDGYVLGASIVGPEASELIAELCLAIELGATLEDVASTVHAHPTLSESVMEAAENALG 479

Query: 468 QAIHTLNR 475
            AIHTLNR
Sbjct: 480 HAIHTLNR 487


Lambda     K      H
   0.315    0.134    0.381 

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: 881
Number of extensions: 45
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: 475
Length of database: 487
Length adjustment: 34
Effective length of query: 441
Effective length of database: 453
Effective search space:   199773
Effective search space used:   199773
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_076582962.1 BB347_RS13020 (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.2899784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-162  527.0   1.4   2.7e-162  526.6   1.4    1.1  1  NCBI__GCF_001971705.1:WP_076582962.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001971705.1:WP_076582962.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.6   1.4  2.7e-162  2.7e-162       2     460 ..      10     483 ..       9     484 .. 0.95

  Alignments for each domain:
  == domain 1  score: 526.6 bits;  conditional E-value: 2.7e-162
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           +dv+viG+Gp+GYvaAira+ql l v+lveke +GGtCln GCiP+Kal+++++v++ + +a+e+gi++ + +
  NCBI__GCF_001971705.1:WP_076582962.1  10 TDVLVIGAGPAGYVAAIRAGQLDLDVTLVEKEAYGGTCLNHGCIPSKALITATDVAHGAATAEEMGIHA-DPA 81 
                                           79*****************************************************************65.799 PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...kkleakniiiAtGsepr 144
                                           +dl+ ++ +k+ vv++l++Gv+ L+k n+v+ ++G+a+++d+++ +++++ +    ++le++++i+AtGs+p+
  NCBI__GCF_001971705.1:WP_076582962.1  82 IDLSGMVSWKDGVVDQLTSGVEKLCKANQVSLLEGTATFVDEHTARISHSGEGqgsESLEFEHAIVATGSRPI 154
                                           ***********************************************9987556889**************** PP

                             TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvl 217
                                           ++p  +++d + vi+s++al+l++vp+slv+vG+G+iG+E+as++aklG++vtv+e+ld ilp  d ++ + +
  NCBI__GCF_001971705.1:WP_076582962.1 155 AIPD-FSFDADPVIDSRQALALDSVPDSLVVVGAGYIGMELASVYAKLGTDVTVVEMLDSILPGYDDDLKRPV 226
                                           ****.9999999************************************************************* PP

                             TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv...............veakkkevetleaekvLvavGrkpnleelg 275
                                           k++ ++ g++++++++ +e  + +++++               +ea ++e  +l++ekvLvavGr+p  + l+
  NCBI__GCF_001971705.1:WP_076582962.1 227 KQRANDLGIEFVFEHTASEWYEPDEDIRvvaepvdgaaanggsAEAIDEERLELDVEKVLVAVGREPVSDTLD 299
                                           *****************987777776665567777765555544445556678999***************** PP

                             TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviyt 348
                                           le+ gve+d+rg+i++d + rtnv++i+a+GDv+g++mLAh+ s eg  aae iag+ + +id++a+P+v++t
  NCBI__GCF_001971705.1:WP_076582962.1 300 LEAAGVETDDRGIIQTDTRARTNVDHIFAVGDVAGEPMLAHKGSMEGQTAAEVIAGEPA-AIDHQAMPAVVFT 371
                                           ********************************************************776.9************ PP

                             TIGR01350 349 ePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselisela 421
                                           +Pe+a+vGlte++a e+g++ +vg+fpf+a+g+al+++++dGfvk+++++++g +lGa+ivg+easeli+el 
  NCBI__GCF_001971705.1:WP_076582962.1 372 DPEIATVGLTETDAEEAGYDPVVGQFPFRASGRALTTGDADGFVKIVAEESDGYVLGASIVGPEASELIAELC 444
                                           ************************************************************************* PP

                             TIGR01350 422 laveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                           la+el++t+e++a+t+h+HPtlsE ++eaa++alg+aih
  NCBI__GCF_001971705.1:WP_076582962.1 445 LAIELGATLEDVASTVHAHPTLSESVMEAAENALGHAIH 483
                                           **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (487 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: 15.53
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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