Alignments for a candidate for lpd in Limnohabitans curvus MWH-C5

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Limnohabitans curvus MWH-C5

Align dihydrolipoamide dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_108402666.1 B9Z44_RS13470 dihydrolipoyl dehydrogenase

Query= metacyc::MONOMER-18551
         (613 letters)



>NCBI__GCF_003063475.1:WP_108402666.1
          Length = 618

 Score =  809 bits (2089), Expect = 0.0
 Identities = 432/636 (67%), Positives = 501/636 (78%), Gaps = 42/636 (6%)

Query: 1   MSQVEIKVPDIGDFDAVEVIEVLVAQGDTVKEEQSLITVESDKASMEIPSSAAGKVVSLS 60
           M+ ++I+VPDIGDFD V VIE+LV  GDTVK EQSLITVESDKASMEIPSS AG V  L 
Sbjct: 1   MALIDIQVPDIGDFDEVAVIELLVKPGDTVKAEQSLITVESDKASMEIPSSHAGVVKELK 60

Query: 61  VKVGDKVSEGTVILMLEAAAAGAQAAASDKAAAQPAAKSEAAAQKPAASSAAAEQASAAA 120
           VK+GDKV +G+V+L+L+            + AA PAA + AAA  P ++ AAA  ++AA 
Sbjct: 61  VKLGDKVKQGSVVLVLDG-----------EGAAAPAASAPAAAPAPTSAPAAATASAAA- 108

Query: 121 DQRPAQAAADSSEVRYSPPASAPADGCDVLVLGAGPGGYSAAFRAADLGLSVVLVERYAT 180
              PA AAA +  V  S   SA  + CDVLVLG GPGGYSAAFRAADLGL+VV+VERYAT
Sbjct: 109 ---PAVAAAPAP-VASSFGGSADIE-CDVLVLGGGPGGYSAAFRAADLGLNVVIVERYAT 163

Query: 181 LGGVCLNVGCIPSKALLHSVAVLEEAKHLSENGITFGEPAIDLDKLRASKDKVVSTLTGG 240
           LGGVCLNVGCIPSKALLH  AV++E  H+++ G+ FG PA+++DKLR  K+KV+  LTGG
Sbjct: 164 LGGVCLNVGCIPSKALLHVAAVMDEVAHMADLGVDFGTPAVNIDKLRGHKEKVIGKLTGG 223

Query: 241 LTGMAKARKVKVIQGLGQFADEYHL-------TVQKDDGSSETVAFKHAIIAAGSQSVKL 293
           L  MAK RKV  ++GLGQF    HL       T Q+ +GS + +AFK AIIAAGSQ+V+L
Sbjct: 224 LAAMAKMRKVTTVRGLGQFVGANHLEVSETTGTAQEQNGSKKVIAFKKAIIAAGSQAVRL 283

Query: 294 PFLPEDERIIDSTGALKLKSIPKKMLIIGGGIIGLEMGTVYSALGARLDVVEMLDGLMQG 353
           PF+P D R++DSTGAL+LK +PK+MLI+GGGIIGLEMGTVYS LGARLDVVEM+DGLMQG
Sbjct: 284 PFMPNDPRVVDSTGALELKEVPKRMLILGGGIIGLEMGTVYSTLGARLDVVEMMDGLMQG 343

Query: 354 ADRDLVKVWQKKNEGRFDQIMVKTKTVSAEAKPDGIWVKF----EGEAAPAEPQRYDLVL 409
           ADRDLVKVWQK N  RFD IM+KTKTVSA A P+GI V F    EG  APA PQ YDLVL
Sbjct: 344 ADRDLVKVWQKMNAKRFDNIMLKTKTVSARALPEGIEVTFAPAEEGGTAPA-PQVYDLVL 402

Query: 410 QAVGRSPNGAKIGADKAGVQVTERGFINVDEQMRTNVPHIFAIGDIVGQPMLAHKAVHEA 469
           QAVGR+PNG K+ ADKAGV VT+RGFINVD QMRTNVPHIFAIGDIVGQPMLAHKAVHEA
Sbjct: 403 QAVGRTPNGKKLAADKAGVSVTDRGFINVDIQMRTNVPHIFAIGDIVGQPMLAHKAVHEA 462

Query: 470 HVAAEVIAGH--------KSYFDVRVIPSVAYTDPEVAWAGLTEEEAKKQGIKFEKGVFP 521
           HVAAEVIAG          + F+ RVIPSVAYTDPEVAW GLTE++AK QGIK +KG+FP
Sbjct: 463 HVAAEVIAGELQGNKELAAAAFNARVIPSVAYTDPEVAWVGLTEDQAKAQGIKVKKGLFP 522

Query: 522 WAASGRAIANGRSEGFTKLLFD--AETH---RIIGGSIVGTHAGDLISEVALAVEMGADS 576
           W ASGRAIANGR EG TKLLFD   E H   +I+GG +VGTHAGD+I E+ALA+EMGAD+
Sbjct: 523 WTASGRAIANGRDEGVTKLLFDDSPEAHGHGKILGGGMVGTHAGDMIGEIALAIEMGADA 582

Query: 577 VDIGKTIHPHPTLGESVGMAAEVAHGTCTDLPPVKR 612
           VDIGKTIHPHPTLGES+GMAAEVAHG+CTDLPP K+
Sbjct: 583 VDIGKTIHPHPTLGESIGMAAEVAHGSCTDLPPSKK 618


Lambda     K      H
   0.314    0.131    0.364 

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: 1035
Number of extensions: 37
Number of successful extensions: 6
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: 613
Length of database: 618
Length adjustment: 37
Effective length of query: 576
Effective length of database: 581
Effective search space:   334656
Effective search space used:   334656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate WP_108402666.1 B9Z44_RS13470 (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.3742364.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-140  453.9   7.4   3.8e-140  453.5   7.4    1.1  1  NCBI__GCF_003063475.1:WP_108402666.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003063475.1:WP_108402666.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.5   7.4  3.8e-140  3.8e-140       2     456 ..     130     608 ..     129     612 .. 0.93

  Alignments for each domain:
  == domain 1  score: 453.5 bits;  conditional E-value: 3.8e-140
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                            dv+v+GgGpgGY aA raa lgl+v++ve+  +lGG+ClnvGCiP+KalL+ a v++e+ ++++lg++  + 
  NCBI__GCF_003063475.1:WP_108402666.1 130 CDVLVLGGGPGGYSAAFRAADLGLNVVIVERyATLGGVCLNVGCIPSKALLHVAAVMDEVAHMADLGVDFGTP 202
                                           79*****************************99**************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kkleakniiiA 138
                                           +++++kl  +kekv+ kl+gG++a+ k  kv+++ G +++++++++ev++++++        k++ +k++iiA
  NCBI__GCF_003063475.1:WP_108402666.1 203 AVNIDKLRGHKEKVIGKLTGGLAAMAKMRKVTTVRGLGQFVGANHLEVSETTGTaqeqngskKVIAFKKAIIA 275
                                           *************************************************99887888999989999******* PP

                             TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpalda 211
                                            Gs+  +lp+ + +d  +v++s++alelkevp++++i+GgG+iG+E+++++++lG+ + v+e++d +++  d+
  NCBI__GCF_003063475.1:WP_108402666.1 276 AGSQAVRLPF-MPNDP-RVVDSTGALELKEVPKRMLILGGGIIGLEMGTVYSTLGARLDVVEMMDGLMQGADR 346
                                           **********.87776.7******************************************************* PP

                             TIGR01350 212 evskvlkkklkkkgvkiltnakvtevekeedevv.....veakkkevetleaekvLvavGrkpnleelglekl 279
                                           ++ kv +k+  k+  +i+ ++k  + ++  + ++     +e+ ++      ++ vL avGr+pn ++l  +k 
  NCBI__GCF_003063475.1:WP_108402666.1 347 DLVKVWQKMNAKRFDNIMLKTKTVSARALPEGIEvtfapAEEGGTAPAPQVYDLVLQAVGRTPNGKKLAADKA 419
                                           *********9999989999988887776666666334433333335566789********************* PP

                             TIGR01350 280 gveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.......eidykavPsv 345
                                           gv++++rg+i+vd ++rtnvp+i+aiGD++g++mLAh+A++e+ vaae iag+ +        +++++++Psv
  NCBI__GCF_003063475.1:WP_108402666.1 420 GVSVTDRGFINVDIQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVIAGELQGnkelaaaAFNARVIPSV 492
                                           ***************************************************98766678999999******** PP

                             TIGR01350 346 iytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkk.....tgeilGahivgaea 413
                                            yt+Peva vGlte+qak++gi+vk g fp +a+g+a+a + ++G+ k+++d +      g+ilG  +vg++a
  NCBI__GCF_003063475.1:WP_108402666.1 493 AYTDPEVAWVGLTEDQAKAQGIKVKKGLFPWTASGRAIANGRDEGVTKLLFDDSpeahgHGKILGGGMVGTHA 565
                                           ***************************************************97633333689*********** PP

                             TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                            ++i e+ala+e+++ + ++ ktihpHPtl+E i  aa+ a g
  NCBI__GCF_003063475.1:WP_108402666.1 566 GDMIGEIALAIEMGADAVDIGKTIHPHPTLGESIGMAAEVAHG 608
                                           ***********************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (618 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: 35.76
//
[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:

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