Alignments for a candidate for lpd in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas stutzeri RCH2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate GFF2444 Psest_2492 dihydrolipoamide dehydrogenase

Query= SwissProt::P18925
         (477 letters)



>FitnessBrowser__psRCH2:GFF2444
          Length = 478

 Score =  819 bits (2115), Expect = 0.0
 Identities = 411/477 (86%), Positives = 447/477 (93%)

Query: 1   MSQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSKAL 60
           MSQKFDV+VIGAGPGGYVAAI++AQLGLKTA IEKY+GK+GKTALGGTCLNVGCIPSKAL
Sbjct: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYQGKDGKTALGGTCLNVGCIPSKAL 60

Query: 61  LDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLFEG 120
           LDSSYKFHEAHESFK+HGISTGEVA+DVPTM+ARKDQIV+NLTGGV++L+KANGVT+FEG
Sbjct: 61  LDSSYKFHEAHESFKVHGISTGEVAMDVPTMVARKDQIVKNLTGGVSALLKANGVTVFEG 120

Query: 121 HGKLLAGKKVEVTAADGSSQVLDTENVILASGSKPVEIPPAPVDQDVIVDSTGALDFQNV 180
           HGKLLAGK+VEVT  DG+ Q L  ENVILASGS PV IPPAPVDQ VIVDSTGALDFQ V
Sbjct: 121 HGKLLAGKQVEVTGLDGNVQTLAAENVILASGSTPVNIPPAPVDQKVIVDSTGALDFQGV 180

Query: 181 PGKLGVIGAGVIGLELGSVWARLGAEVTVLEAMDKFLPAVDEQVAKEAQKILTKQGLKIL 240
           PGKLGVIGAGVIGLELGSVWARLGAEVTV+EAMDKFLPA DEQ++KEA KIL+KQGLKIL
Sbjct: 181 PGKLGVIGAGVIGLELGSVWARLGAEVTVIEAMDKFLPAADEQISKEAFKILSKQGLKIL 240

Query: 241 LGARVTGTEVKNKQVTVKFVDAEGEKSQAFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300
           LGAR+TG+EVK  QVTV F  AEGE+   FDKLIVAVGRRPVT++LLAAD+GV +DERGF
Sbjct: 241 LGARLTGSEVKGDQVTVSFTSAEGEQQMTFDKLIVAVGRRPVTSELLAADTGVDMDERGF 300

Query: 301 IYVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVVVAERIAGHKAQMNYDLIPAVIYTH 360
           I+VDDYCATSVPGVYAIGDVVRGAMLAHKASEEGV+VAERIAGHK QMNYDLIP+VIYTH
Sbjct: 301 IFVDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVMVAERIAGHKTQMNYDLIPSVIYTH 360

Query: 361 PEIAGVGKTEQALKAEGVAINVGVFPFAASGRAMAANDTAGFVKVIADAKTDRVLGVHVI 420
           PEIA VGK+EQ LKAEGV +NVG FPFAASGRAMAANDTAG VKVIADAKTDRVLGVHV+
Sbjct: 361 PEIAWVGKSEQVLKAEGVEVNVGTFPFAASGRAMAANDTAGLVKVIADAKTDRVLGVHVM 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFAHPALSEALHEAALAVSGHAIHVANRKK 477
           GPSAAELVQQGAI MEFGTSAEDLGMMVF+HP +SEALHEAALAV+GHAIH+ANRKK
Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTMSEALHEAALAVNGHAIHIANRKK 477


Lambda     K      H
   0.316    0.134    0.372 

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: 839
Number of extensions: 29
Number of successful extensions: 1
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: 477
Length of database: 478
Length adjustment: 34
Effective length of query: 443
Effective length of database: 444
Effective search space:   196692
Effective search space used:   196692
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 GFF2444 Psest_2492 (dihydrolipoamide 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.29910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-167  542.9  10.9   3.4e-167  542.7  10.9    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2444  Psest_2492 dihydrolipoamide dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2444  Psest_2492 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.7  10.9  3.4e-167  3.4e-167       1     461 []       4     472 ..       4     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 542.7 bits;  conditional E-value: 3.4e-167
                           TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevveelke.akelg 67 
                                         ++dvvviG+GpgGYvaAiraaqlglk+a++ek +       lGGtClnvGCiP+KalL s+  ++e++e +k +g
  lcl|FitnessBrowser__psRCH2:GFF2444   4 KFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKyQgkdgktALGGTCLNVGCIPSKALLDSSYKFHEAHEsFKVHG 78 
                                         59*****************************74222333369***************************9***** PP

                           TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGs 141
                                         i++ +v++d+ ++++rk+++vk+l+gGv+aLlk n+v+v++G++kll  k+vev++ +++ ++l a+n+i+A+Gs
  lcl|FitnessBrowser__psRCH2:GFF2444  79 ISTGEVAMDVPTMVARKDQIVKNLTGGVSALLKANGVTVFEGHGKLLAGKQVEVTGLDGNvQTLAAENVILASGS 153
                                         ********************************************************998889************* PP

                           TIGR01350 142 eprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                         +p ++p    +d+kv+++s++al ++ vp +l ++G+GviG+E++s++a+lG++vtvie++d+ lpa d+++sk+
  lcl|FitnessBrowser__psRCH2:GFF2444 154 TPVNIPP-APVDQKVIVDSTGALDFQGVPGKLGVIGAGVIGLELGSVWARLGAEVTVIEAMDKFLPAADEQISKE 227
                                         ******9.9999999************************************************************ PP

                           TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaik 290
                                         + k l+k+g+kil +a++t  e + d+v+v+  +   +++++ +k++vavGr+p ++el  + +gv++derg+i 
  lcl|FitnessBrowser__psRCH2:GFF2444 228 AFKILSKQGLKILLGARLTGSEVKGDQVTVSFTSAeGEQQMTFDKLIVAVGRRPVTSELLAADTGVDMDERGFIF 302
                                         *******************9999*****988777756799*********************************** PP

                           TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakee 365
                                         vd+++ t+vpg+yaiGDv++++mLAh+As+egv++ae+iag+++ +++y+++Psviyt+Pe+a vG++e+ +k+e
  lcl|FitnessBrowser__psRCH2:GFF2444 303 VDDYCATSVPGVYAIGDVVRGAMLAHKASEEGVMVAERIAGHKT-QMNYDLIPSVIYTHPEIAWVGKSEQVLKAE 376
                                         *****************************************666.9***************************** PP

                           TIGR01350 366 gievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpH 440
                                         g+ev+vg fpfaa+g+a+a+++t G+vkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e+l ++++ H
  lcl|FitnessBrowser__psRCH2:GFF2444 377 GVEVNVGTFPFAASGRAMAANDTAGLVKVIADAKTDRVLGVHVMGPSAAELVQQGAIGMEFGTSAEDLGMMVFSH 451
                                         *************************************************************************** PP

                           TIGR01350 441 PtlsEaikeaalaalgkaihv 461
                                         Pt+sEa++eaala++g+aih+
  lcl|FitnessBrowser__psRCH2:GFF2444 452 PTMSEALHEAALAVNGHAIHI 472
                                         *******************96 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: 00:00:00.01
# Mc/sec: 12.47
//
[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:

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