GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Caulobacter crescentus NA1000

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate CCNA_00346 CCNA_00346 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__Caulo:CCNA_00346
          Length = 466

 Score =  643 bits (1658), Expect = 0.0
 Identities = 311/465 (66%), Positives = 377/465 (81%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M  YDV++IG GPGGYNAAIRAGQLGLKVA VEGR  LGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MAQYDVVIIGGGPGGYNAAIRAGQLGLKVAIVEGRGKLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
           AAA+G EFA+LGI V P+L+L+QMM QK ESV ALT+GVEFL +K+KV+++KGW R+ G 
Sbjct: 61  AAATGPEFAKLGIEVKPKLNLSQMMAQKAESVEALTKGVEFLMKKNKVEYVKGWGRIDGV 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V   DG    LE ++IVIATGSEP PLPGV VDN+RI+DSTGAL L EVP+ LVV+
Sbjct: 121 GKVVVKAEDGSETTLETKNIVIATGSEPTPLPGVSVDNKRIIDSTGALSLPEVPKRLVVV 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVW+RLGA+VTV+EYL+RI PG D E A   Q+ L +QG +F+LG +V  
Sbjct: 181 GAGVIGLELGSVWKRLGAEVTVVEYLDRILPGTDTEVANAFQKILVKQGFKFQLGAKVTG 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +G +GV+L  +P AGG  ++++ADYVLVAIGRRPYT+GLGLETVG+  D+RGM+ N  
Sbjct: 241 AEAGAKGVKLSFEPVAGGEAQTIEADYVLVAIGRRPYTQGLGLETVGVTPDKRGMIANDH 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            ++   GVWVIGDVTSGPMLAHKAE+E + CIE IAG A  +N  +IP V+YT PEVA+V
Sbjct: 301 FKTGVAGVWVIGDVTSGPMLAHKAEDEGVACIEMIAGKAGHVNYGIIPGVVYTSPEVATV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  E++L+A    YKVG+FPF ANSRAKINHE++GF+KIL+DA++D++LG HMIGP V +
Sbjct: 361 GKTEDELKAEGVAYKVGKFPFLANSRAKINHETDGFVKILADAKTDRILGAHMIGPNVGD 420

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MI E CVAMEF  ++ED+A TCHPHPTRSEALRQAAM V G  MQ
Sbjct: 421 MIAEYCVAMEFGGASEDVARTCHPHPTRSEALRQAAMGVEGWTMQ 465


Lambda     K      H
   0.318    0.135    0.390 

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: 794
Number of extensions: 27
Number of successful extensions: 1
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: 467
Length of database: 466
Length adjustment: 33
Effective length of query: 434
Effective length of database: 433
Effective search space:   187922
Effective search space used:   187922
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_00346 CCNA_00346 (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.6137.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-168  547.0   7.7   1.9e-168  546.8   7.7    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00346  CCNA_00346 dihydrolipoamide dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00346  CCNA_00346 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.8   7.7  1.9e-168  1.9e-168       1     456 [.       3     461 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 546.8 bits;  conditional E-value: 1.9e-168
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelgiev 70 
                                           +ydvv+iGgGpgGY aAira+qlglkva+ve   klGGtClnvGC+P+KalL+++e+++ ++   +++lgiev
  lcl|FitnessBrowser__Caulo:CCNA_00346   3 QYDVVIIGGGPGGYNAAIRAGQLGLKVAIVEGrGKLGGTCLNVGCMPSKALLHASELYAAATGpeFAKLGIEV 75 
                                           69*****************************879*************************9987679*****98 PP

                             TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGse 142
                                            + kl+l++++++k + v+ l++Gv++L+kknkve +kG +++ + ++v vk+e+++ ++le+kni+iAtGse
  lcl|FitnessBrowser__Caulo:CCNA_00346  76 -KPKLNLSQMMAQKAESVEALTKGVEFLMKKNKVEYVKGWGRIDGVGKVVVKAEDGSeTTLETKNIVIATGSE 147
                                           .79**************************************************99886899************ PP

                             TIGR01350 143 prelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevsk 215
                                           p+ lp+ +++d+k++i+s++al+l+evp++lv+vG+GviG+E++s++++lG++vtv+e+ldrilp +d+ev++
  lcl|FitnessBrowser__Caulo:CCNA_00346 148 PTPLPG-VSVDNKRIIDSTGALSLPEVPKRLVVVGAGVIGLELGSVWKRLGAEVTVVEYLDRILPGTDTEVAN 219
                                           ******.999999************************************************************ PP

                             TIGR01350 216 vlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelde 285
                                           + +k l k+g k+  +akvt  e+ ++ v+  +e   + e++t+ea++vLva+Gr+p +++lgle++gv+ d+
  lcl|FitnessBrowser__Caulo:CCNA_00346 220 AFQKILVKQGFKFQLGAKVTGAEAGAKGVKlsFEPVAGgEAQTIEADYVLVAIGRRPYTQGLGLETVGVTPDK 292
                                           ********************99999999995555444459********************************* PP

                             TIGR01350 286 rgaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlt 358
                                           rg+i  +++++t v+g+++iGDv++++mLAh+A++egv ++e iagk+  +++y  +P v+yt+Peva+vG+t
  lcl|FitnessBrowser__Caulo:CCNA_00346 293 RGMI-ANDHFKTGVAGVWVIGDVTSGPMLAHKAEDEGVACIEMIAGKAG-HVNYGIIPGVVYTSPEVATVGKT 363
                                           **76.699**************************************998.9********************** PP

                             TIGR01350 359 eeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431
                                           e+++k+eg+++kvgkfpf an++a + +etdGfvk+++d kt++ilGah++g+++ ++i+e  +a+e+++ +e
  lcl|FitnessBrowser__Caulo:CCNA_00346 364 EDELKAEGVAYKVGKFPFLANSRAKINHETDGFVKILADAKTDRILGAHMIGPNVGDMIAEYCVAMEFGGASE 436
                                           ************************************************************************* PP

                             TIGR01350 432 elaktihpHPtlsEaikeaalaalg 456
                                           ++a+t+hpHPt sEa+ +aa  + g
  lcl|FitnessBrowser__Caulo:CCNA_00346 437 DVARTCHPHPTRSEALRQAAMGVEG 461
                                           *******************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 11.95
//
[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