Alignments for a candidate for lpd in Caulobacter crescentus NA1000

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.23210.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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 10.25
//
[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:

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 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