GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Bacillus altitudinis 41KF2b

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of acetoin cleaving system (uncharacterized)
to candidate WP_035704233.1 BA79_RS17615 dihydrolipoyl dehydrogenase

Query= curated2:O34324
         (458 letters)



>NCBI__GCF_000691145.1:WP_035704233.1
          Length = 459

 Score =  553 bits (1424), Expect = e-162
 Identities = 273/458 (59%), Positives = 349/458 (76%), Gaps = 1/458 (0%)

Query: 1   MTLAIIGGGPAGYAAAVSAAQQGRNVLLIDKGKLGGTCLNEGCIPTKSLLESANVLDKIK 60
           MTL IIGGGPAGY AA++AA+  R V+LID+G LGGTCLNEGCIPTK+LL+SA++ + +K
Sbjct: 1   MTLVIIGGGPAGYVAAITAARFDREVVLIDQGLLGGTCLNEGCIPTKALLQSADMYEHVK 60

Query: 61  HADSFGIELPAGAISVDWSKMQSRKQQVVSQLVQGVQYLMKKNQIQVVKGTASFLSERKL 120
            A  FGIELP     + W  +Q RK+ VV QL  GV+YLM KN+I V+ G ASFLS  +L
Sbjct: 61  SAGHFGIELPGKEPVIHWDAVQKRKRSVVKQLTDGVRYLMNKNKISVLNGKASFLSAHEL 120

Query: 121 LIEGENGKEIREADQVLIASGSEPIELPFAPFDGEWILDSKDALSLSEIPSSLVIVGGGV 180
           LIE E   EI +A Q++IASGSEP  LPFAPFD EWI+DSKDA++L  IP SL I+GGGV
Sbjct: 121 LIESEGKSEIIQAKQIIIASGSEPAALPFAPFDREWIIDSKDAMTLPSIPDSLCIIGGGV 180

Query: 181 IGCEYAGLFARLGSQVTIIETADRLIPAEDEDIARLFQEKLEEDGVEVHTSSRLGRVDQT 240
           IGCE+A +F+R+GS+V ++E A  ++P ED D A    ++L++ GVE+ TS+ + ++D +
Sbjct: 181 IGCEFASIFSRMGSKVVMVEQAAHILPEEDYDTANCLYDQLQKAGVEILTSAAVKQLDAS 240

Query: 241 AKTAIWKSGQRE-FKTKADYVLVAIGRKPRLDGLQLEQAGVDFSPKGIPVNGHMQTNVPH 299
           +K  + +    E    ++D+ LVAIGRKPRL  L LEQ G++F   GI VN HMQTN+ H
Sbjct: 241 SKKVVVEKDHGERCDIQSDHCLVAIGRKPRLGELNLEQIGIEFDRNGICVNEHMQTNLSH 300

Query: 300 IYACGDAIGGIQLAHAAFHEGIIAASHASGRDVKINEKHVPRCIYTSPEIACIGMTERQA 359
           IYACGD  GG+QLAHAAFHEG IAASHASG DVK+NE+ +PRCIYTSPEIA +G+ E  A
Sbjct: 301 IYACGDVTGGVQLAHAAFHEGTIAASHASGEDVKVNEQVIPRCIYTSPEIASVGLNEENA 360

Query: 360 RSIYGDVKIGEFSFSANGKALIKQQAEGKVKIMAEPEFGEIVGVSMIGPDVTELIGQAAA 419
           R  YG+++IG+F+FSANGKALI  Q  G+VK++ EP++ EI+GVS+IGP+ TELIGQAA 
Sbjct: 361 RKQYGEIRIGKFAFSANGKALILNQPAGQVKVIVEPQYQEILGVSIIGPNATELIGQAAV 420

Query: 420 IMNGEMTADMAEHFIAAHPTLSETLHEALLSTIGLAVH 457
           +M+ E+TAD  E FIAAHPTLSE +HEALL T G AVH
Sbjct: 421 MMHTELTADTLEQFIAAHPTLSEAIHEALLQTNGRAVH 458


Lambda     K      H
   0.316    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: 600
Number of extensions: 34
Number of successful extensions: 2
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: 458
Length of database: 459
Length adjustment: 33
Effective length of query: 425
Effective length of database: 426
Effective search space:   181050
Effective search space used:   181050
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: 51 (24.3 bits)

Align candidate WP_035704233.1 BA79_RS17615 (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.2793283.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-173  561.5   4.5   7.7e-173  561.3   4.5    1.0  1  NCBI__GCF_000691145.1:WP_035704233.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035704233.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.3   4.5  7.7e-173  7.7e-173       4     460 ..       3     458 ..       1     459 [] 0.98

  Alignments for each domain:
  == domain 1  score: 561.3 bits;  conditional E-value: 7.7e-173
                             TIGR01350   4 vvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven..vk 74 
                                           +v+iGgGp+GYvaAi+aa+   +v+l+++  lGGtCln+GCiPtKalL+sa+++e++k a ++gie+ +    
  NCBI__GCF_000691145.1:WP_035704233.1   3 LVIIGGGPAGYVAAITAARFDREVVLIDQGLLGGTCLNEGCIPTKALLQSADMYEHVKSAGHFGIELPGkePV 75 
                                           89****************************************************************8776799 PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           + ++++++rk++vvk+l++Gv++L++knk++v++G+a++l+++e+ +++e k++ ++ak+iiiA+Gsep++lp
  NCBI__GCF_000691145.1:WP_035704233.1  76 IHWDAVQKRKRSVVKQLTDGVRYLMNKNKISVLNGKASFLSAHELLIESEGKSEIIQAKQIIIASGSEPAALP 148
                                           ***************************************************99******************** PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                           +   +d++ +i+s++a++l+++p+sl i+GgGviG+Efasif+++G+kv ++e + +ilp +d + ++ l ++
  NCBI__GCF_000691145.1:WP_035704233.1 149 F-APFDREWIIDSKDAMTLPSIPDSLCIIGGGVIGCEFASIFSRMGSKVVMVEQAAHILPEEDYDTANCLYDQ 220
                                           *.7777777**************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                           l+k gv+ilt+a v+++ +++++vvve++++e   +++++ Lva+Grkp+l el+le++g+e+d++g i v+e
  NCBI__GCF_000691145.1:WP_035704233.1 221 LQKAGVEILTSAAVKQLDASSKKVVVEKDHGERCDIQSDHCLVAIGRKPRLGELNLEQIGIEFDRNG-ICVNE 292
                                           ***************************9999**********************************77.***** PP

                             TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                           +++tn+++iya+GDv+g+++LAh A++eg++aa ++ g+   +++++++P++iyt+Pe+asvGl+ee+a++++
  NCBI__GCF_000691145.1:WP_035704233.1 293 HMQTNLSHIYACGDVTGGVQLAHAAFHEGTIAASHASGED-VKVNEQVIPRCIYTSPEIASVGLNEENARKQY 364
                                           **************************************66.59****************************** PP

                             TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                            e+++gkf f+angkal+l++  G vkviv+++++eilG++i+g++a+eli ++a+++++elt++ l+++i +
  NCBI__GCF_000691145.1:WP_035704233.1 365 GEIRIGKFAFSANGKALILNQPAGQVKVIVEPQYQEILGVSIIGPNATELIGQAAVMMHTELTADTLEQFIAA 437
                                           ************************************************************************* PP

                             TIGR01350 440 HPtlsEaikeaalaalgkaih 460
                                           HPtlsEai+ea+l+++g+a+h
  NCBI__GCF_000691145.1:WP_035704233.1 438 HPTLSEAIHEALLQTNGRAVH 458
                                           *******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (459 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: 14.94
//
[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