GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc01035 SMc01035 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Smeli:SMc01035
          Length = 481

 Score =  513 bits (1321), Expect = e-150
 Identities = 264/480 (55%), Positives = 334/480 (69%), Gaps = 15/480 (3%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA+++D+IV+G GPGGYV AIR+AQL LK A+VER HLGGICLNWGCIPTK+LLRSAE+ 
Sbjct: 1   MAENYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEIL 60

Query: 61  HEMQNAEAYGLT-SFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGN 119
               +A+ YGLT   K   ++  ++ARSR V+ RL  GV  L++KNKV+VI G  +LT  
Sbjct: 61  DHANHAKNYGLTLEGKITANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKP 120

Query: 120 QQMLVETTEGE--------------EKILEAKDIIIATGARARQLPNVHSDGKHIWTYHH 165
            +++V                    E    AK II+ATGAR R LP +  DGK IWTY  
Sbjct: 121 GEIVVGAPSKPAVQPQNPVPKGVKGEGTYTAKHIIVATGARPRALPGIEPDGKLIWTYFE 180

Query: 166 ALKPPAMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFK 225
           A+KP   PK LLV+GSGAIGIEFASFY   G +V++VE  PQI+P+EDAE+SA+  K  +
Sbjct: 181 AMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVEDAEISAFARKQLE 240

Query: 226 KRGIRILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLG 285
           KRG++I+T + +  +      VTA +   DGKVT  +    I A+GV  N+EN+GL+ LG
Sbjct: 241 KRGLKIITDAKVTKVEKGANDVTAHVETKDGKVTPIKADRLISAVGVQGNIENLGLEALG 300

Query: 286 IKLDRGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQ 345
           +K DRG I  DG+G+TNV  ++AIGDVAG P LAHKA H+GVI  E IAG   VH L+  
Sbjct: 301 VKTDRGCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVHALDKG 360

Query: 346 NIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADS 405
            IPGCTY  PQVASVGLTE KA++ G ++++G + F ANGKAIA G   G +KT+FD  +
Sbjct: 361 KIPGCTYCDPQVASVGLTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKT 420

Query: 406 GALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           G L+GAHMVGAEVTE+IQG+ VA  LETTE E+M T+FPHPTLSE M ESVL AYGR L+
Sbjct: 421 GELIGAHMVGAEVTELIQGFVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVLN 480


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: 721
Number of extensions: 31
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: 481
Length adjustment: 33
Effective length of query: 433
Effective length of database: 448
Effective search space:   193984
Effective search space used:   193984
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 SMc01035 SMc01035 (dihydrolipoamide 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.27422.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.9e-180  585.8   6.6   3.3e-180  585.6   6.6    1.0  1  lcl|FitnessBrowser__Smeli:SMc01035  SMc01035 dihydrolipoamide dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01035  SMc01035 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.6   6.6  3.3e-180  3.3e-180       1     459 [.       4     479 ..       4     481 .] 0.97

  Alignments for each domain:
  == domain 1  score: 585.6 bits;  conditional E-value: 3.3e-180
                           TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven.vk 74 
                                         +ydv+v+G+GpgGYv+Air+aqlglk+a+ve+e+lGG+Cln+GCiPtKalL+sae+++++++ak++g+++e+ ++
  lcl|FitnessBrowser__Smeli:SMc01035   4 NYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEILDHANHAKNYGLTLEGkIT 78 
                                         69*******************************************************************9999** PP

                           TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...............kkleakn 134
                                          +++++++r++ v+ +l+gGv++L+kknkv+vi+Geakl++++e+ v + +k                 +++ak+
  lcl|FitnessBrowser__Smeli:SMc01035  79 ANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKPGEIVVGAPSKPavqpqnpvpkgvkgeGTYTAKH 153
                                         ***********************************************8877556889999999998878899*** PP

                           TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpal 209
                                         ii+AtG++pr+lp+ +e d+k+++t+ ea++ +e+p+sl+++G+G+iG+Efas+++++Gv+vtv+ell++i+p++
  lcl|FitnessBrowser__Smeli:SMc01035 154 IIVATGARPRALPG-IEPDGKLIWTYFEAMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVE 227
                                         **************.************************************************************ PP

                           TIGR01350 210 daevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgve 282
                                         dae+s +++k+l+k+g+ki+t+akvt+vek +++v+  ve+k+++v+ ++a++++ avG++ n+e+lgle+lgv+
  lcl|FitnessBrowser__Smeli:SMc01035 228 DAEISAFARKQLEKRGLKIITDAKVTKVEKGANDVTahVETKDGKVTPIKADRLISAVGVQGNIENLGLEALGVK 302
                                         ************************************888888889****************************** PP

                           TIGR01350 283 ldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvG 356
                                         +d+ g+i++d + +tnv+giyaiGDv+g++mLAh+A++egv+++ekiag     ++d+ ++P ++y++P+vasvG
  lcl|FitnessBrowser__Smeli:SMc01035 303 TDR-GCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVhALDKGKIPGCTYCDPQVASVG 376
                                         776.*********************************************9988799******************* PP

                           TIGR01350 357 lteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431
                                         lte++ake g +++vg+++f angka+al+e++G++k+i+dkktge++Gah+vgae++eli+ +++a++le+t+e
  lcl|FitnessBrowser__Smeli:SMc01035 377 LTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKTGELIGAHMVGAEVTELIQGFVVAMNLETTEE 451
                                         *************************************************************************** PP

                           TIGR01350 432 elaktihpHPtlsEaikeaalaalgkai 459
                                         el++t++pHPtlsE++ke++l+a+g+ +
  lcl|FitnessBrowser__Smeli:SMc01035 452 ELMHTVFPHPTLSEMMKESVLDAYGRVL 479
                                         ***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (481 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: 11.15
//
[ok]

This GapMind analysis is from Sep 17 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