GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Phaeobacter inhibens BS107

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate GFF3862 PGA1_78p00260 dihydrolipoyl dehydrogenase LpdA

Query= curated2:P95596
         (454 letters)



>FitnessBrowser__Phaeo:GFF3862
          Length = 460

 Score =  492 bits (1266), Expect = e-143
 Identities = 257/461 (55%), Positives = 337/461 (73%), Gaps = 8/461 (1%)

Query: 1   MAEFDVIIIGGGPGGYVCAIRCAQLGLKTACVEGRGALGGTCLNVGCIPSKALLHATHEL 60
           M+ +D+I+IGGGPGGYV AIR AQLGLK ACVEGRG LGGTCLNVGCIPSKA+L ++ + 
Sbjct: 1   MSLYDLIVIGGGPGGYVAAIRAAQLGLKVACVEGRGTLGGTCLNVGCIPSKAMLSSSGKY 60

Query: 61  HEV-HENFEKMGLMGAKVKVDWA-----KIDGN-TKGIEFLFKKNKVTYLRGWGSIPAPG 113
             + H     + + GA++ +D       KI G+ TKGI FLF+KN V  + GW SIPA G
Sbjct: 61  ESLSHLAGHGIAIEGARLDLDAMMARKDKIVGDLTKGIAFLFQKNGVDLIEGWASIPAVG 120

Query: 114 QVKVGDEVHTAKNIVIATGSESSGLPGIEIDEQTVVTSTGALSLAKVPKSMVVIGAGVIG 173
           +VKVGDE+H  KNI+IATGSE + LPG+EIDE  VV+STGAL+L +VPK +VV+GAGVIG
Sbjct: 121 KVKVGDEIHETKNILIATGSEPTPLPGVEIDEGDVVSSTGALTLPEVPKHLVVVGAGVIG 180

Query: 174 LELGSVYARLGAEVTVVEYLDAITPGMDAEVAKGLQRILTRQGLKFVLGAAVQGVDKAKG 233
           LELG V++RLGA+VTVVEYLD I PG+D E+AK  QR L+++GLKF LG A++ +D++  
Sbjct: 181 LELGQVWSRLGAKVTVVEYLDRILPGIDGEIAKLAQRALSKRGLKFQLGRALKFIDRSDE 240

Query: 234 KNTVRYTLRKDESAHAIEAEVVLVATGRKPFTKGLGLEALGVEMLPRGQVKADSHWATNV 293
             T+       +    + A+ VL+A GR+P  +GLGLEALGV +  RG V+ D  ++T+V
Sbjct: 241 GLTLTLDRVGKDKEEQLVADKVLIAIGRRPVIRGLGLEALGVSVNARGFVEVDERFSTSV 300

Query: 294 PGLYAIGDAIVGPMLAHKAEDEGMAVAEVIAGKHGHVNYDVIPGVIYTTPEVAAVGKTED 353
            G+YAIGD + GPMLAHKAE++G+A  E++AG+ GHV+Y+ +PG++YT PEVA+VGKTE+
Sbjct: 301 EGIYAIGDCVPGPMLAHKAEEDGVACVEMLAGQAGHVDYNTVPGIVYTDPEVASVGKTEE 360

Query: 354 ALKQEGRAYKVGKFSFMGNGRAKAVFQAEGFVKILADAATDRILGAHIIGPSAGDMIHEI 413
           ALK  G  Y VGKF FM N RA+A  + +G VK+LA     +ILGAHI G   GD+I E+
Sbjct: 361 ALKDAGTDYIVGKFIFMANSRARAQGETDGAVKVLA-TPEGQILGAHICGAHGGDLIAEL 419

Query: 414 CVAMEFGASAQDLALTCHAHPTYSEAVREAALACGDGAIHA 454
            +AM  GA+  ++A TCHAHP  +EAV+EA L     AIHA
Sbjct: 420 VLAMTKGATVAEVAATCHAHPAMAEAVKEACLDAMGRAIHA 460


Lambda     K      H
   0.318    0.136    0.397 

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: 783
Number of extensions: 30
Number of successful extensions: 4
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: 454
Length of database: 460
Length adjustment: 33
Effective length of query: 421
Effective length of database: 427
Effective search space:   179767
Effective search space used:   179767
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF3862 PGA1_78p00260 (dihydrolipoyl dehydrogenase LpdA)
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.1403142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.5e-167  541.8   5.0   7.4e-167  541.6   5.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3862  PGA1_78p00260 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3862  PGA1_78p00260 dihydrolipoyl dehydrogenase LpdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.6   5.0  7.4e-167  7.4e-167       2     460 ..       4     459 ..       3     460 .] 0.97

  Alignments for each domain:
  == domain 1  score: 541.6 bits;  conditional E-value: 7.4e-167
                          TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkld 76 
                                        yd++viGgGpgGYvaAiraaqlglkva+ve   +lGGtClnvGCiP+Ka+L s+  +e+l++++ +gi +e+ +ld
  lcl|FitnessBrowser__Phaeo:GFF3862   4 YDLIVIGGGPGGYVAAIRAAQLGLKVACVEGrGTLGGTCLNVGCIPSKAMLSSSGKYESLSHLAGHGIAIEGARLD 79 
                                        9*****************************8789****************************************** PP

                          TIGR01350  77 lekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152
                                        l+++++rk+k+v  l++G+++L++kn+v+ i+G a++   ++v+v +e +    e+kni+iAtGsep+ lp+ +e 
  lcl|FitnessBrowser__Phaeo:GFF3862  80 LDAMMARKDKIVGDLTKGIAFLFQKNGVDLIEGWASIPAVGKVKVGDEIH----ETKNILIATGSEPTPLPG-VEI 150
                                        *********************************************99974....6*****************.999 PP

                          TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228
                                        de  v++s++al+l+evp++lv+vG+GviG+E+++++++lG+kvtv+e+ldrilp +d e++k+++++l+k+g+k+
  lcl|FitnessBrowser__Phaeo:GFF3862 151 DEGDVVSSTGALTLPEVPKHLVVVGAGVIGLELGQVWSRLGAKVTVVEYLDRILPGIDGEIAKLAQRALSKRGLKF 226
                                        9999************************************************************************ PP

                          TIGR01350 229 ltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpg 301
                                          +  ++ + ++++ ++  + + +k ++e+l a+kvL+a+Gr+p +++lgle+lgv+++ rg+++vde++ t+v+g
  lcl|FitnessBrowser__Phaeo:GFF3862 227 QLGRALKFIDRSDEGLTltLDRVGKdKEEQLVADKVLIAIGRRPVIRGLGLEALGVSVNARGFVEVDERFSTSVEG 302
                                        *******9999999988665566666889*********************************************** PP

                          TIGR01350 302 iyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfa 377
                                        iyaiGD++ ++mLAh+A+++gv ++e +ag++  ++dy++vP ++yt+PevasvG+tee +k++g+++ vgkf f+
  lcl|FitnessBrowser__Phaeo:GFF3862 303 IYAIGDCVPGPMLAHKAEEDGVACVEMLAGQAG-HVDYNTVPGIVYTDPEVASVGKTEEALKDAGTDYIVGKFIFM 377
                                        ******************************998.9***************************************** PP

                          TIGR01350 378 angkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453
                                        an++a+a++etdG vkv++ ++ g+ilGahi ga+  +li+el+la++ ++tv e+a+t+h+HP+++Ea+kea+l+
  lcl|FitnessBrowser__Phaeo:GFF3862 378 ANSRARAQGETDGAVKVLATPE-GQILGAHICGAHGGDLIAELVLAMTKGATVAEVAATCHAHPAMAEAVKEACLD 452
                                        *****************99886.89*************************************************** PP

                          TIGR01350 454 algkaih 460
                                        a+g+aih
  lcl|FitnessBrowser__Phaeo:GFF3862 453 AMGRAIH 459
                                        ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (460 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: 00:00:00.00
# Mc/sec: 23.81
//
[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