Alignments for a candidate for lpd in Phaeobacter inhibens BS107

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.30602.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.09
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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