Alignments for a candidate for lpd in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Sinorhizobium medicae WSM419

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011975257.1 SMED_RS05405 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000017145.1:WP_011975257.1
          Length = 481

 Score =  514 bits (1323), Expect = e-150
 Identities = 265/480 (55%), Positives = 335/480 (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  DHANHAKNYGLTLEGKITANVKDVVARSRAVSARLNGGVAFLMKKNKVDVIWGEAKLTKP 120

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

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

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

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

Query: 346 NIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADS 405
            IPGCTY  PQVASVGLTE +A++ G +V++G + F ANGKAIA G   G +KT+FD  +
Sbjct: 361 KIPGCTYCDPQVASVGLTEARAKELGRDVRVGRYSFNANGKAIALGEDQGLIKTIFDKMT 420

Query: 406 GALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           G LLGAHMVGAEVTE+IQG+ VA  LETTE E+M T+FPHPTLSE M ESVL AYGR L+
Sbjct: 421 GELLGAHMVGAEVTELIQGFVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVLN 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: 711
Number of extensions: 30
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 WP_011975257.1 SMED_RS05405 (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.2855300.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-181  587.6   3.8   9.5e-181  587.4   3.8    1.0  1  NCBI__GCF_000017145.1:WP_011975257.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017145.1:WP_011975257.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.4   3.8  9.5e-181  9.5e-181       1     459 [.       4     479 ..       4     481 .] 0.97

  Alignments for each domain:
  == domain 1  score: 587.4 bits;  conditional E-value: 9.5e-181
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven. 72 
                                           +ydv+v+G+GpgGYv+Air+aqlglk+a+ve+e+lGG+Cln+GCiPtKalL+sae+++++++ak++g+++e+ 
  NCBI__GCF_000017145.1:WP_011975257.1   4 NYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEILDHANHAKNYGLTLEGk 76 
                                           69*******************************************************************9999 PP

                             TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke...............kkl 130
                                           ++ +++++++r+++v+ +l+gGv++L+kknkv+vi+Geakl++++e+ v + ++                 ++
  NCBI__GCF_000017145.1:WP_011975257.1  77 ITANVKDVVARSRAVSARLNGGVAFLMKKNKVDVIWGEAKLTKPGEIVVGSPSRPavqpqnpvpkgvkgeGTY 149
                                           ************************************************9887654678889999999887889 PP

                             TIGR01350 131 eakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielld 203
                                           +ak+ii+AtG++pr+lp+ +e d+k+++t+ ea++  e+p+sl+++G+G+iG+Efas+++++Gv+vtviell+
  NCBI__GCF_000017145.1:WP_011975257.1 150 TAKHIILATGARPRALPG-IEPDGKLIWTYFEAMKPAEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVIELLP 221
                                           9*****************.****************************************************** PP

                             TIGR01350 204 rilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleel 274
                                           +i+p++dae+s +++k+l+k+g+ki+t+akvt+vek +++v+  ve+k+++v+ ++ae+++ avG++ n+e+l
  NCBI__GCF_000017145.1:WP_011975257.1 222 QIMPVEDAEISAFARKQLEKRGLKIITDAKVTKVEKGANDVTahVETKDGKVTPMKAERLISAVGVQGNIENL 294
                                           ******************************************888888889********************** PP

                             TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsvi 346
                                           gle+lg+++d+ g+i++d + +tnvpgiyaiGDv+g++mLAh+A++egv+++ekiag     ++d+ ++P ++
  NCBI__GCF_000017145.1:WP_011975257.1 295 GLEALGIKTDR-GCIVTDGYGKTNVPGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVhALDKGKIPGCT 366
                                           ********776.*********************************************9988799********* PP

                             TIGR01350 347 ytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselise 419
                                           y++P+vasvGlte+ ake g +v+vg+++f+angka+al+e++G++k+i+dk tge+lGah+vgae++eli+ 
  NCBI__GCF_000017145.1:WP_011975257.1 367 YCDPQVASVGLTEARAKELGRDVRVGRYSFNANGKAIALGEDQGLIKTIFDKMTGELLGAHMVGAEVTELIQG 439
                                           ************************************************************************* PP

                             TIGR01350 420 lalaveleltveelaktihpHPtlsEaikeaalaalgkai 459
                                           +++a++le+t+eel++t++pHPtlsE++ke++l+a+g+ +
  NCBI__GCF_000017145.1:WP_011975257.1 440 FVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.37
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources