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) (characterized)
to candidate WP_017367571.1 BA79_RS11110 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000691145.1:WP_017367571.1
          Length = 474

 Score =  380 bits (977), Expect = e-110
 Identities = 206/475 (43%), Positives = 300/475 (63%), Gaps = 10/475 (2%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA  +DL++LGGG GGYVAAIRA+QL LK A+VE+  LGG CL+ GCIP+K+LLRSAEVY
Sbjct: 1   MATEYDLVILGGGTGGYVAAIRASQLGLKTAVVEKSKLGGTCLHKGCIPSKALLRSAEVY 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
             ++ A  +G+ +         +  R  E+  +LA GVK L+++ K++V  G+G++ G  
Sbjct: 61  QTVKRAADFGVEASGIALQFASVQKRKTEIVDKLAGGVKHLMKQGKIDVYEGIGRILGPS 120

Query: 121 -------QMLVETTEGEE-KILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAM 172
                   + VE   G+E ++L  K +IIATG+R R LP + +DG HI T   AL+   +
Sbjct: 121 IFSPMPGTISVEMANGDENEMLIPKQVIIATGSRPRVLPGLEADGTHILTSDEALELQEL 180

Query: 173 PKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRIL 232
           P+ +L++G G IGIE+AS   DFG +V+++E A +ILP ED ++S  + K   K+GI ++
Sbjct: 181 PQSMLIVGGGVIGIEWASMLNDFGVKVTVIEFADRILPTEDQDISKEMEKLLTKKGITLV 240

Query: 233 TQSALQNLTPDDEGVTAEIAGADGKVTKE-RFSHAIVAIGVVANVENIGLDKLGIKLDRG 291
           T + +   T +      +I    G  T+       ++++G V NVE IGL+   I+ +  
Sbjct: 241 TNAKVLPDTAEKHENLVKIQVEQGGDTQSFEAEKLLLSVGRVPNVEGIGLENTDIQTENH 300

Query: 292 FIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCT 351
            I V+   +T   H++AIGDV G   LAH ASH+G+IA E +AG D   PL+   +  C 
Sbjct: 301 GIVVNEHYQTKESHIYAIGDVIGGLQLAHVASHEGMIAVEHMAGQDP-KPLDETLVSKCV 359

Query: 352 YARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGA 411
           Y+ P+ ASVGLTE+ A++QGY VKIG FPF+A GKA+  G +DGFVK + D  +  +LG 
Sbjct: 360 YSHPETASVGLTEQAAKEQGYEVKIGKFPFMAIGKALVFGESDGFVKIIADQKTDDILGI 419

Query: 412 HMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           HM+G  VT+MI    +A+ L+ T  E+ +TI PHPTLSEA+ E+ LA  G+A+HF
Sbjct: 420 HMIGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAVDGKAIHF 474


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: 594
Number of extensions: 28
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: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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_017367571.1 BA79_RS11110 (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.1609082.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-183  597.0   9.2   1.3e-183  596.8   9.2    1.0  1  NCBI__GCF_000691145.1:WP_017367571.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_017367571.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.8   9.2  1.3e-183  1.3e-183       1     461 []       4     474 .]       4     474 .] 0.98

  Alignments for each domain:
  == domain 1  score: 596.8 bits;  conditional E-value: 1.3e-183
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           eyd+v++GgG+gGYvaAira+qlglk+a+vek+klGGtCl++GCiP+KalL+saev++++k a+++g+e++++
  NCBI__GCF_000691145.1:WP_017367571.1   4 EYDLVILGGGTGGYVAAIRASQLGLKTAVVEKSKLGGTCLHKGCIPSKALLRSAEVYQTVKRAADFGVEASGI 76 
                                           69*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld.......kkevevkkekke..kkleakniii 137
                                           +l+++++++rk+++v+kl+gGvk+L+k+ k++v++G +++l+       +++++v++ ++   ++l  k++ii
  NCBI__GCF_000691145.1:WP_017367571.1  77 ALQFASVQKRKTEIVDKLAGGVKHLMKQGKIDVYEGIGRILGpsifspmPGTISVEMANGDenEMLIPKQVII 149
                                           *****************************************99999999899999988877679999****** PP

                             TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210
                                           AtGs+pr lp+ le+d++ ++ts+ealel+e+p+s++ivGgGviG+E+as+++++Gvkvtvie++drilp++d
  NCBI__GCF_000691145.1:WP_017367571.1 150 ATGSRPRVLPG-LEADGTHILTSDEALELQELPQSMLIVGGGVIGIEWASMLNDFGVKVTVIEFADRILPTED 221
                                           ***********.************************************************************* PP

                             TIGR01350 211 aevskvlkkklkkkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklg 280
                                           +++sk+++k l+kkg++++tnakv   + ek+e+ v+++ +++ ++++ eaek+L++vGr pn+e++gle+++
  NCBI__GCF_000691145.1:WP_017367571.1 222 QDISKEMEKLLTKKGITLVTNAKVLpdTAEKHENLVKIQVEQGgDTQSFEAEKLLLSVGRVPNVEGIGLENTD 294
                                           ************************997888888889999988889**************************** PP

                             TIGR01350 281 veldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePeva 353
                                           ++++++g i+v+e+++t+ ++iyaiGDvig+l+LAhvAs+eg++a+e++ag+ ++ +d+++v +++y++Pe a
  NCBI__GCF_000691145.1:WP_017367571.1 295 IQTENHG-IVVNEHYQTKESHIYAIGDVIGGLQLAHVASHEGMIAVEHMAGQDPKPLDETLVSKCVYSHPETA 366
                                           **99977.***************************************************************** PP

                             TIGR01350 354 svGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalavel 426
                                           svGlte+ ake+g+evk+gkfpf+a+gkal+ +e+dGfvk+i+d+kt++ilG+h++g++++++ise+ la  l
  NCBI__GCF_000691145.1:WP_017367571.1 367 SVGLTEQAAKEQGYEVKIGKFPFMAIGKALVFGESDGFVKIIADQKTDDILGIHMIGPHVTDMISEAGLAKVL 439
                                           ************************************************************************* PP

                             TIGR01350 427 eltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                           ++t +e+ +tihpHPtlsEai eaala+ gkaih+
  NCBI__GCF_000691145.1:WP_017367571.1 440 DATPWEVGQTIHPHPTLSEAIGEAALAVDGKAIHF 474
                                           *********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (474 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: 16.85
//
[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