Alignments for a candidate for lpd in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Rhizorhabdus wittichii RW1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011950421.1 SWIT_RS24900 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000016765.1:WP_011950421.1
          Length = 465

 Score =  581 bits (1497), Expect = e-170
 Identities = 288/465 (61%), Positives = 354/465 (76%), Gaps = 1/465 (0%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MAD +D+IVLG GPGGYVAAIRAAQL L  A+VER +LGG+CLNWGCIPTK+LLRSAEV+
Sbjct: 1   MADSYDVIVLGSGPGGYVAAIRAAQLKLNTAIVERENLGGVCLNWGCIPTKALLRSAEVF 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
             M++A+ YGL + K   DLD ++ RSR VA +L  GV  L++KN + V  G G+LTG  
Sbjct: 61  RYMRHAKDYGLVAEKITADLDAVVKRSRGVARQLNQGVSHLMKKNGIAVYMGEGKLTGKG 120

Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180
           ++ V   +G+   L AK+IIIATGARAR LP   +DGK +WTY HA+ PP MP KLLVIG
Sbjct: 121 RLSVTAPDGKTSELTAKNIIIATGARARDLPFPKADGKRVWTYRHAMNPPEMPNKLLVIG 180

Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240
           SGAIGIEFASFY D GAEV++VE   +I+P+EDA+VS ++ KA  K+G++ILT + +Q L
Sbjct: 181 SGAIGIEFASFYNDMGAEVTVVEMLDRIVPVEDADVSTFLEKALVKQGMKILTGAGVQKL 240

Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGR 300
                GVT  I   DGK+  + +SH IVAIG+V N E +GL+ LG+K +RG I  DG  R
Sbjct: 241 DIGATGVTVAIKARDGKLVSDEYSHVIVAIGIVPNTETVGLEALGVKTERGHIVTDGACR 300

Query: 301 TNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASV 360
           TNV+ +WAIGD    P LAHKASH+GVIAAE IAG  H H ++ +NIPGCTY  PQ+ASV
Sbjct: 301 TNVEGIWAIGDATAPPWLAHKASHEGVIAAETIAG-QHPHAMDPRNIPGCTYCHPQIASV 359

Query: 361 GLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTE 420
           GLTE  AR+ G+ V+IG FPFI NGKAIA G  +GFVKTVFDA +G LLGAHMVG EVTE
Sbjct: 360 GLTETNAREAGHEVRIGTFPFIGNGKAIALGEPEGFVKTVFDAQTGELLGAHMVGPEVTE 419

Query: 421 MIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           MI G+T+ RTLETTEAE+MET+FPHPT+SE MHESVLAA+GRA+H
Sbjct: 420 MIHGFTIGRTLETTEAELMETVFPHPTISETMHESVLAAFGRAVH 464


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: 688
Number of extensions: 29
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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_011950421.1 SWIT_RS24900 (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.3803554.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-176  572.6   2.6   3.3e-176  572.4   2.6    1.0  1  NCBI__GCF_000016765.1:WP_011950421.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_011950421.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.4   2.6  3.3e-176  3.3e-176       1     461 []       4     465 .]       4     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: 572.4 bits;  conditional E-value: 3.3e-176
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           +ydv+v+G+GpgGYvaAiraaql+l++a+ve+e+lGG+Cln+GCiPtKalL+saev++++++ak++g+ +e++
  NCBI__GCF_000016765.1:WP_011950421.1   4 SYDVIVLGSGPGGYVAAIRAAQLKLNTAIVERENLGGVCLNWGCIPTKALLRSAEVFRYMRHAKDYGLVAEKI 76 
                                           59*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepre 145
                                           + dl+++++r++ v ++l++Gv++L+kkn++ v++Ge+kl++k++++v++ +++ ++l+akniiiAtG++ r 
  NCBI__GCF_000016765.1:WP_011950421.1  77 TADLDAVVKRSRGVARQLNQGVSHLMKKNGIAVYMGEGKLTGKGRLSVTAPDGKtSELTAKNIIIATGARARD 149
                                           *************************************************988776899*************** PP

                             TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218
                                           lp+  ++d+k+v+t+++a++ +e+p++l+++G+G+iG+Efas+++++G++vtv+e+ldri+p++da+vs +l+
  NCBI__GCF_000016765.1:WP_011950421.1 150 LPF-PKADGKRVWTYRHAMNPPEMPNKLLVIGSGAIGIEFASFYNDMGAEVTVVEMLDRIVPVEDADVSTFLE 221
                                           ***.8889999************************************************************** PP

                             TIGR01350 219 kklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergai 289
                                           k+l k+g+kilt+a v+++   +  v+v +k +  +  + e+ +v+va+G  pn+e +gle+lgv++ erg i
  NCBI__GCF_000016765.1:WP_011950421.1 222 KALVKQGMKILTGAGVQKLDIGATGVTVAIKARdgKLVSDEYSHVIVAIGIVPNTETVGLEALGVKT-ERGHI 293
                                           *****************999999999965555522666677889**********************5.56*** PP

                             TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqa 362
                                           ++d  +rtnv+gi+aiGD+++++ LAh+As+egv+aae+iag++++++d + +P ++y++P++asvGlte++a
  NCBI__GCF_000016765.1:WP_011950421.1 294 VTDGACRTNVEGIWAIGDATAPPWLAHKASHEGVIAAETIAGQHPHAMDPRNIPGCTYCHPQIASVGLTETNA 366
                                           ************************************************************************* PP

                             TIGR01350 363 keegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelak 435
                                           +e+g+ev++g fpf  ngka+al+e +Gfvk+++d +tge+lGah+vg+e++e+i+ +++  +le+t+ el++
  NCBI__GCF_000016765.1:WP_011950421.1 367 REAGHEVRIGTFPFIGNGKAIALGEPEGFVKTVFDAQTGELLGAHMVGPEVTEMIHGFTIGRTLETTEAELME 439
                                           ************************************************************************* PP

                             TIGR01350 436 tihpHPtlsEaikeaalaalgkaihv 461
                                           t++pHPt+sE+++e++laa+g+a+h+
  NCBI__GCF_000016765.1:WP_011950421.1 440 TVFPHPTISETMHESVLAAFGRAVHI 465
                                           ***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.46
//
[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