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_01805 CCNA_01805 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Caulo:CCNA_01805
          Length = 466

 Score =  484 bits (1245), Expect = e-141
 Identities = 252/470 (53%), Positives = 328/470 (69%), Gaps = 10/470 (2%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           M+  FD++V+G GPGGYVAAIRA+QL L  A++ER +LGGICLNWGCIPTK+LL+S EVY
Sbjct: 1   MSTEFDVVVIGAGPGGYVAAIRASQLGLNTAIIERENLGGICLNWGCIPTKALLKSGEVY 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
            ++ +   YGL+  K  FD  KII RSR VA  ++ G+  L++K+K+EVI G  +L    
Sbjct: 61  EQLSHLGGYGLSVEKASFDFGKIIERSRGVAKNMSGGIAFLMKKHKIEVIEGEAKLEKGA 120

Query: 121 ---QMLVETTEGEEKILEAKDIIIATGARARQLPNVH--SDGKHIWTYHHALKPPAMPKK 175
              +++V    G  + ++AK++I+A+GARAR++P +   SDG  IWTY  AL P +MPK 
Sbjct: 121 PAPKVVVALKAGGSRTVQAKNVILASGARAREIPAIGAVSDGDKIWTYRDALAPKSMPKS 180

Query: 176 LLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQS 235
           L+VIGSGAIGIEFASFY   GAEV++VE   +I+P+ED EVS    KAF+KRGI+    +
Sbjct: 181 LVVIGSGAIGIEFASFYRALGAEVTVVEAIDRIMPVEDEEVSKAAQKAFEKRGIKFRVGA 240

Query: 236 ALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAV 295
            +  +    +GV   +  A GK+ +      IVA+G+  N  N GL+ LG+ LDRG +  
Sbjct: 241 KVSKIEKTKDGVAVTVE-AGGKIEQLTAEKCIVAVGIAPN--NDGLEALGVSLDRGHVVT 297

Query: 296 DGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARP 355
           D   RTNV  ++AIGD+AGAP LAHKASH+G+ AAEAIAG    + L+   IPGCTYA P
Sbjct: 298 DKHCRTNVPGLYAIGDIAGAPWLAHKASHEGIHAAEAIAGYKTPNVLSP--IPGCTYANP 355

Query: 356 QVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVG 415
           QVASVG TE  A+  G  VK G FPF  NGKA+A G T+GFVKTVFDA +GAL+GAHM+G
Sbjct: 356 QVASVGYTEAGAKAAGIEVKAGRFPFRVNGKAVASGETEGFVKTVFDAKTGALIGAHMIG 415

Query: 416 AEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
            EVTEMIQG+  A TLE TE ++   ++ HPT+SEAMHE+ L AYGR LH
Sbjct: 416 HEVTEMIQGFVTAITLEATEEDLHGVVYAHPTMSEAMHEAALDAYGRVLH 465


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: 654
Number of extensions: 33
Number of successful extensions: 5
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: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 CCNA_01805 CCNA_01805 (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.23137.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.2e-170  551.5  10.9   8.1e-170  551.3  10.9    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01805  CCNA_01805 dihydrolipoamide dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01805  CCNA_01805 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.3  10.9  8.1e-170  8.1e-170       1     460 [.       4     465 ..       4     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 551.3 bits;  conditional E-value: 8.1e-170
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           e+dvvviG+GpgGYvaAira+qlgl++a++e+e+lGG+Cln+GCiPtKalLks+ev+e+l+++  +g++ve+ 
  lcl|FitnessBrowser__Caulo:CCNA_01805   4 EFDVVVIGAGPGGYVAAIRASQLGLNTAIIERENLGGICLNWGCIPTKALLKSGEVYEQLSHLGGYGLSVEKA 76 
                                           69*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld...kkevevkkekke.kkleakniiiAtGse 142
                                           ++d+ k+ er++ v k+++gG+++L+kk+k+evi+Geakl++   + +v v+ +++  ++++akn+i+A+G++
  lcl|FitnessBrowser__Caulo:CCNA_01805  77 SFDFGKIIERSRGVAKNMSGGIAFLMKKHKIEVIEGEAKLEKgapAPKVVVALKAGGsRTVQAKNVILASGAR 149
                                           *****************************************977755677766655459************** PP

                             TIGR01350 143 prelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevs 214
                                            re+p     +d++ ++t+++al+ k++p+slv++G+G+iG+Efas+++ lG++vtv+e+ dri+p++d+evs
  lcl|FitnessBrowser__Caulo:CCNA_01805 150 AREIPAIgAVSDGDKIWTYRDALAPKSMPKSLVVIGSGAIGIEFASFYRALGAEVTVVEAIDRIMPVEDEEVS 222
                                           ******987777789********************************************************** PP

                             TIGR01350 215 kvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgvelder 286
                                           k+++k+++k+g+k+  +akv+++ek++d v v+ + + ++e+l+aek +vavG  pn +  gle+lgv+ld+ 
  lcl|FitnessBrowser__Caulo:CCNA_01805 223 KAAQKAFEKRGIKFRVGAKVSKIEKTKDGVAVTVEAGgKIEQLTAEKCIVAVGIAPNND--GLEALGVSLDR- 292
                                           *******************************88887779********************..*********98. PP

                             TIGR01350 287 gaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlte 359
                                           g +++d+++rtnvpg+yaiGD++g + LAh+As+eg+ aae+iag ++     + +P ++y++P+vasvG+te
  lcl|FitnessBrowser__Caulo:CCNA_01805 293 GHVVTDKHCRTNVPGLYAIGDIAGAPWLAHKASHEGIHAAEAIAGYKT-PNVLSPIPGCTYANPQVASVGYTE 364
                                           *********************************************776.78899******************* PP

                             TIGR01350 360 eqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltvee 432
                                           + ak++gievk+g+fpf+ ngka+a++et+Gfvk+++d ktg+++Gah++g e++e+i+ ++ a++le+t+e+
  lcl|FitnessBrowser__Caulo:CCNA_01805 365 AGAKAAGIEVKAGRFPFRVNGKAVASGETEGFVKTVFDAKTGALIGAHMIGHEVTEMIQGFVTAITLEATEED 437
                                           ************************************************************************* PP

                             TIGR01350 433 laktihpHPtlsEaikeaalaalgkaih 460
                                           l+ ++++HPt+sEa++eaal+a+g+ +h
  lcl|FitnessBrowser__Caulo:CCNA_01805 438 LHGVVYAHPTMSEAMHEAALDAYGRVLH 465
                                           ************************9998 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.22
//
[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