GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate PfGW456L13_4267 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267
          Length = 478

 Score =  854 bits (2207), Expect = 0.0
 Identities = 436/478 (91%), Positives = 455/478 (95%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           M+QKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGKLALGGTCLNVGCIPSKAL
Sbjct: 1   MSQKFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKYTDKEGKLALGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDSSWK+ EA++ F +HGI+   V MDV AMVGRKA IVK LT GVATLFKANGVTSIQG
Sbjct: 61  LDSSWKFHEAQDGFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
           HGKLLAGKKVEVTK DG+ E+IEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V
Sbjct: 121 HGKLLAGKKVEVTKPDGSVEIIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVW+RLGAEVTVLEALDTFLMAADTAVSKEA KTLTKQGLDIK
Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADTAVSKEALKTLTKQGLDIK 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           LGARVTGSKVNG+EV V YT+A+GEQ ITFDKLIVAVGRRPVTTDLLAAD GVT+DERG+
Sbjct: 241 LGARVTGSKVNGDEVVVNYTDAKGEQNITFDKLIVAVGRRPVTTDLLAADCGVTLDERGF 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           + VDD+CAT+VPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH
Sbjct: 301 VHVDDHCATTVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI
Sbjct: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIH+ANRKKR
Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHIANRKKR 478


Lambda     K      H
   0.316    0.133    0.374 

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: 890
Number of extensions: 18
Number of successful extensions: 2
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: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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 PfGW456L13_4267 (Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4))
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.30790.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   9.3e-165  534.7  10.5   1.1e-164  534.5  10.5    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267  Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenas
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.5  10.5  1.1e-164  1.1e-164       1     461 []       4     472 ..       4     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 534.5 bits;  conditional E-value: 1.1e-164
                                               TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtK 48 
                                                             ++dvvviG+GpgGYvaAi+aaqlgl++a++ek  +k     lGGtClnvGCiP+K
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267   4 KFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKytDKegklaLGGTCLNVGCIPSK 58 
                                                             59*****************************95421344449************* PP

                                               TIGR01350  49 alLksaevveelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkkn 102
                                                             alL s+  ++e+++ ++ +gi+ ++v++d+ +++ rk ++vk l++Gv++L+k n
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267  59 ALLDSSWKFHEAQDgFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKAN 113
                                                             ******************************************************* PP

                                               TIGR01350 103 kvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleedekv 156
                                                             +v++i+G++kll  k+vev+k +++ + +ea+n+i+A Gs+p+ +p    +d++v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 114 GVTSIQGHGKLLAGKKVEVTKPDGSvEIIEAENVILAPGSRPIDIPP-APVDQNV 167
                                                             *********************9988899******************9.8999999 PP

                                               TIGR01350 157 vitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpalda 211
                                                             +++s++ale+++vp++l ++G+GviG+E++s++++lG++vtv+e+ld+ l a d+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 168 IVDSTGALEFQSVPKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADT 222
                                                             ******************************************************* PP

                                               TIGR01350 212 evskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvav 265
                                                              vsk++ k+l+k+g++i+ +a+vt  + + devvv+  +   +++++ +k++vav
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 223 AVSKEALKTLTKQGLDIKLGARVTGSKVNGDEVVVNYTDAkGEQNITFDKLIVAV 277
                                                             ************************99999999996666554679*********** PP

                                               TIGR01350 266 GrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAsk 320
                                                             Gr+p +++l  +  gv+lderg+++vd+++ t+vpg+yaiGDv++++mLAh+As+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 278 GRRPVTTDLLAADCGVTLDERGFVHVDDHCATTVPGVYAIGDVVRGMMLAHKASE 332
                                                             ******************************************************* PP

                                               TIGR01350 321 egvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfp 375
                                                             eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+eg+ev+vg fp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 333 EGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQALKAEGVEVNVGTFP 386
                                                             ***********665.9*************************************** PP

                                               TIGR01350 376 faangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltv 430
                                                             faa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 387 FAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSA 441
                                                             ******************************************************* PP

                                               TIGR01350 431 eelaktihpHPtlsEaikeaalaalgkaihv 461
                                                             e+l ++++ HPtlsEa++eaala++g aih+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 442 EDLGMMVFSHPTLSEALHEAALAVNGGAIHI 472
                                                             *****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (478 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: 00:00:00.02
# Mc/sec: 10.43
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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