GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Marinicella litoralis KMM 3900

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_099019200.1 CCS90_RS08975 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_002591915.1:WP_099019200.1
          Length = 473

 Score =  513 bits (1320), Expect = e-150
 Identities = 264/475 (55%), Positives = 345/475 (72%), Gaps = 3/475 (0%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           M +K+DVVVIG GP GYVAAIRAAQ+G  T C++++ GK+GK +LGGTCLNVGCIPSKAL
Sbjct: 1   MMEKYDVVVIGGGPAGYVAAIRAAQMGFNTLCVDRFKGKDGKYSLGGTCLNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           LDSS  +     ++ VHGI      +DV  M+ARK  IVK LTGGIA LFKAN V    G
Sbjct: 61  LDSSKHFDHMNHSYDVHGISFDNPKMDVATMIARKDKIVKQLTGGIAQLFKANKVKYIGG 120

Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180
            GKLL ++QVE+   +G +QV++ E++I+ASGS P+ IP   + ++ I+D+ GAL+  AV
Sbjct: 121 SGKLLKDRQVEINNDEG-SQVVQGEHIILASGSVPISIPNVEIDNEYILDNAGALDINAV 179

Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240
           P+KLGVIG GVIGLELGSVW RLG++V V EA+D FL A D+ IAK A +   KQGL+I 
Sbjct: 180 PEKLGVIGGGVIGLELGSVWNRLGSKVKVFEAMDTFLAACDQGIAKMAARTFKKQGLDIH 239

Query: 241 LGARVTASEVKKKQVTVTFTDANGEQ-KETFDKLIVAVGRRPVTTDLLAADSGVTLDERG 299
           L   V ++ +K  +V V  ++ NGE+  E FDKL+VAVGR+  T  LLA D G+ L ERG
Sbjct: 240 LSTFVKSATIKDGKVEVV-SETNGEKTTEIFDKLLVAVGRKAETDGLLADDCGIKLTERG 298

Query: 300 FIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYT 359
            I V+D C+TSVP V+AIGD VRG MLAHK SEEG  VAERIAG    ++++ +P VIYT
Sbjct: 299 QIDVNDDCQTSVPNVWAIGDAVRGPMLAHKGSEEGSAVAERIAGQHGHVDFNTVPFVIYT 358

Query: 360 HPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHV 419
            PE+AWVGKTE+ LK  G++  VG+FP AA+GRA+A N+ TG+VK++ADA+TD +LG H+
Sbjct: 359 EPELAWVGKTEEQLKEAGIDYKVGSFPMAANGRALAMNEPTGMVKILADAETDELLGAHI 418

Query: 420 IGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474
              +AA+L+ +  + MEF   AEDL  ++ +HPTLSEA+ EAA+ V+  AIH AN
Sbjct: 419 FSANAADLLSECVVTMEFKGCAEDLSRIIHAHPTLSEAVFEAAMNVDKRAIHKAN 473


Lambda     K      H
   0.316    0.134    0.375 

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: 629
Number of extensions: 23
Number of successful extensions: 3
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: 478
Length of database: 473
Length adjustment: 33
Effective length of query: 445
Effective length of database: 440
Effective search space:   195800
Effective search space used:   195800
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_099019200.1 CCS90_RS08975 (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.1854001.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-164  533.4   4.7   2.6e-164  533.2   4.7    1.0  1  NCBI__GCF_002591915.1:WP_099019200.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099019200.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.2   4.7  2.6e-164  2.6e-164       1     460 [.       4     470 ..       4     471 .. 0.97

  Alignments for each domain:
  == domain 1  score: 533.2 bits;  conditional E-value: 2.6e-164
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevveelke.ake 65 
                                           +ydvvviGgGp+GYvaAiraaq+g+++++v+       k +lGGtClnvGCiP+KalL s++ ++++++  + 
  NCBI__GCF_002591915.1:WP_099019200.1   4 KYDVVVIGGGPAGYVAAIRAAQMGFNTLCVDrfkgkdgKYSLGGTCLNVGCIPSKALLDSSKHFDHMNHsYDV 76 
                                           59****************************944333333479***************************999* PP

                             TIGR01350  66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiA 138
                                           +gi+ +n k+d++++ +rk+k+vk+l+gG+++L+k nkv+ i G++kll++++ve+++++++++++ ++ii+A
  NCBI__GCF_002591915.1:WP_099019200.1  77 HGISFDNPKMDVATMIARKDKIVKQLTGGIAQLFKANKVKYIGGSGKLLKDRQVEINNDEGSQVVQGEHIILA 149
                                           ************************************************************************* PP

                             TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpalda 211
                                           +Gs p+++p  +e d+++++++ +al ++ vpe+l ++GgGviG+E++s++++lG+kv v+e++d+ l+a d+
  NCBI__GCF_002591915.1:WP_099019200.1 150 SGSVPISIPN-VEIDNEYILDNAGALDINAVPEKLGVIGGGVIGLELGSVWNRLGSKVKVFEAMDTFLAACDQ 221
                                           **********.************************************************************** PP

                             TIGR01350 212 evskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgvel 283
                                            ++k++++++kk+g++i+ ++ v++ + ++ +v+v  + + e++t   +k+LvavGrk+++++l  +  g++l
  NCBI__GCF_002591915.1:WP_099019200.1 222 GIAKMAARTFKKQGLDIHLSTFVKSATIKDGKVEVVSETNgEKTTEIFDKLLVAVGRKAETDGLLADDCGIKL 294
                                           ************************999999999955555547888899************************* PP

                             TIGR01350 284 dergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvG 356
                                           +erg+i v+++++t+vp+++aiGD+++++mLAh+ s+eg  +ae+iag++  ++d ++vP viytePe+a vG
  NCBI__GCF_002591915.1:WP_099019200.1 295 TERGQIDVNDDCQTSVPNVWAIGDAVRGPMLAHKGSEEGSAVAERIAGQHG-HVDFNTVPFVIYTEPELAWVG 366
                                           ************************************************998.9******************** PP

                             TIGR01350 357 lteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalavelelt 429
                                           +teeq+ke+gi++kvg+fp+aang+ala++e +G+vk+++d +t+e+lGahi +a+a++l+se ++ +e+++ 
  NCBI__GCF_002591915.1:WP_099019200.1 367 KTEEQLKEAGIDYKVGSFPMAANGRALAMNEPTGMVKILADAETDELLGAHIFSANAADLLSECVVTMEFKGC 439
                                           ************************************************************************* PP

                             TIGR01350 430 veelaktihpHPtlsEaikeaalaalgkaih 460
                                           +e+l+++ih+HPtlsEa+ eaa ++ ++aih
  NCBI__GCF_002591915.1:WP_099019200.1 440 AEDLSRIIHAHPTLSEAVFEAAMNVDKRAIH 470
                                           *****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (473 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.16
//
[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:

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