GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Algoriphagus aquaeductus T4

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_111392719.1 CLV31_RS09800 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_123536
         (491 letters)



>NCBI__GCF_003253485.1:WP_111392719.1
          Length = 465

 Score =  486 bits (1250), Expect = e-142
 Identities = 248/461 (53%), Positives = 332/461 (72%), Gaps = 3/461 (0%)

Query: 26  YDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHLLHQI 85
           YDV+VIG GPGGYVAAI+AAQLG+ TA +EK   LGGTCLNVGCIPSK+LL++S   H  
Sbjct: 2   YDVIVIGSGPGGYVAAIRAAQLGMKTAIVEKYSTLGGTCLNVGCIPSKALLDSSEHYHNA 61

Query: 86  QHEAKERGISIQGEVGVDFPKLMAAKEKAVKQLTGGIEMLFKKNKVDYLKGAGSFVNEKT 145
            H  K  GI+++ ++ VD  ++++ K+  VKQ   GI+ L KKNK+D   G GSFV+  T
Sbjct: 62  AHTFKTHGINLK-DLKVDLAQMISRKDDVVKQNVDGIQFLMKKNKIDVHHGLGSFVDAHT 120

Query: 146 VKVTPIDGSEAQEVEADHIIVATGSEPTPFPGIEIDEERIVTSTGILSLKEVPERLAIIG 205
           VKVT  DGS + +++  +II+ATGS+P   P I++D++R++TST  L +KE+P+ L +IG
Sbjct: 121 VKVTKEDGSSS-DIQGKNIIIATGSKPASLPFIKLDKDRVITSTEALKMKEIPKHLIVIG 179

Query: 206 GGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLDFKLGTKVVKG 265
           GG+IG+E+ SVY RLG+KV+V+EF ++I   MD  + K+ QK L K G DF L  KV   
Sbjct: 180 GGVIGMELGSVYGRLGAKVSVVEFMDSIIPTMDKTMGKELQKSLKKLGFDFYLKHKVTAV 239

Query: 266 ERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKGRLIIDDQ 325
           E  G+ V ++ ++ K G+  +++ D +LV+IGR+P+T+GLN EA G++  ++G++ ++D 
Sbjct: 240 ENTGKEVVVKADNGK-GETIEIKGDYVLVSIGRKPYTDGLNAEAAGVKLTDRGQVEVNDH 298

Query: 326 FKTKHDHIRVIGDVTFGPMLAHKAEEEGIAAAEYIKKGHGHVNYANIPSVMYTHPEVAWV 385
            +T   HI  IGDV  G MLAHKAEEEG+  AE I     H+NY  IP V+YT PEVA V
Sbjct: 299 LQTSVPHIYAIGDVVKGAMLAHKAEEEGVYVAETIAGQKPHINYLLIPGVVYTWPEVAAV 358

Query: 386 GLNEEQLKEQGIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVLGVHIIGPNAGE 445
           G  EEQLKEQG KYKVGKFPF+A+ RA+ +MDTDG VK +ADAET  +LGVH+IGP   +
Sbjct: 359 GYTEEQLKEQGRKYKVGKFPFLASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTAD 418

Query: 446 MIAEAGLALEYGASTEDISRTCHAHPTLSEAFKEAALATFD 486
           MIAEA +A+EY AS EDISR  HAHPT +EAFKEA LA  D
Sbjct: 419 MIAEAVVAMEYRASAEDISRMSHAHPTYTEAFKEACLAATD 459


Lambda     K      H
   0.316    0.135    0.381 

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: 609
Number of extensions: 36
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: 491
Length of database: 465
Length adjustment: 34
Effective length of query: 457
Effective length of database: 431
Effective search space:   196967
Effective search space used:   196967
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_111392719.1 CLV31_RS09800 (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.3599813.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     7e-185  601.0  11.2   7.8e-185  600.9  11.2    1.0  1  NCBI__GCF_003253485.1:WP_111392719.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003253485.1:WP_111392719.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.9  11.2  7.8e-185  7.8e-185       1     457 [.       1     460 [.       1     465 [] 0.98

  Alignments for each domain:
  == domain 1  score: 600.9 bits;  conditional E-value: 7.8e-185
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieve 71 
                                           +ydv+viG+GpgGYvaAiraaqlg+k+a+vek ++lGGtClnvGCiP+KalL s+e ++++ + +k++gi+++
  NCBI__GCF_003253485.1:WP_111392719.1   1 MYDVIVIGSGPGGYVAAIRAAQLGMKTAIVEKySTLGGTCLNVGCIPSKALLDSSEHYHNAAHtFKTHGINLK 73 
                                           59******************************99*************************************** PP

                             TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                           ++k+dl+++  rk+ vvk+ v+G+++L+kknk++v++G ++++d+++v+v+ke+++ + ++ kniiiAtGs+p
  NCBI__GCF_003253485.1:WP_111392719.1  74 DLKVDLAQMISRKDDVVKQNVDGIQFLMKKNKIDVHHGLGSFVDAHTVKVTKEDGSsSDIQGKNIIIATGSKP 146
                                           *****************************************************988799************** PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                           ++lp+ ++ d+++vits+eal++ke+p++l+++GgGviG+E++s++ +lG+kv+v+e++d i+p++d+++ k+
  NCBI__GCF_003253485.1:WP_111392719.1 147 ASLPF-IKLDKDRVITSTEALKMKEIPKHLIVIGGGVIGMELGSVYGRLGAKVSVVEFMDSIIPTMDKTMGKE 218
                                           *****.8888888************************************************************ PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           l+k+lkk g +++ ++kvt+ve++ +evvv+a+++  e+ ++++++vLv++Grkp +++l+ e+ gv+l++rg
  NCBI__GCF_003253485.1:WP_111392719.1 219 LQKSLKKLGFDFYLKHKVTAVENTGKEVVVKADNGkgETIEIKGDYVLVSIGRKPYTDGLNAEAAGVKLTDRG 291
                                           *****************************88766536888899****************************** PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           +++v+++l+t+vp+iyaiGDv++++mLAh+A++egv++ae+iag+++ +i+y ++P v+yt Peva+vG+tee
  NCBI__GCF_003253485.1:WP_111392719.1 292 QVEVNDHLQTSVPHIYAIGDVVKGAMLAHKAEEEGVYVAETIAGQKP-HINYLLIPGVVYTWPEVAAVGYTEE 363
                                           ********************************************998.9************************ PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           q+ke+g ++kvgkfpf a+g+a+a+ +tdG+vkv++d +t+eilG+h++g++ +++i+e+++a+e ++++e++
  NCBI__GCF_003253485.1:WP_111392719.1 364 QLKEQGRKYKVGKFPFLASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIAEAVVAMEYRASAEDI 436
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgk 457
                                           +++ h+HPt++Ea+kea+laa+++
  NCBI__GCF_003253485.1:WP_111392719.1 437 SRMSHAHPTYTEAFKEACLAATDN 460
                                           *******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 17.47
//
[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