Alignments for a candidate for lpd in Marinicella litoralis KMM 3900

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Marinicella litoralis KMM 3900

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_099017805.1 CCS90_RS01865 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_002591915.1:WP_099017805.1
          Length = 575

 Score =  642 bits (1655), Expect = 0.0
 Identities = 342/593 (57%), Positives = 422/593 (71%), Gaps = 22/593 (3%)

Query: 3   VIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVK 62
           + ++K+P+IGDFD V VIEVLVKAGD V+ +QSL+ LESDKA+M++PS  +G +  + V 
Sbjct: 4   ITDIKIPEIGDFDNVPVIEVLVKAGDNVDKDQSLVTLESDKATMEIPSPQSGVIKSMTVS 63

Query: 63  VGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCE 122
            GD+V  G VI T+E       P   +       P P A    P    A    G D   E
Sbjct: 64  EGDQVSIGQVIGTMEVADETE-PKATENQKIKDEPTPKAQ---PVVKQAEVKEG-DYDTE 118

Query: 123 MLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKA 182
           +LV+GAGPGGY+AAFRAADLGM+  LVERY +LGGVCLNVGCIPSKALLH AAVI E + 
Sbjct: 119 LLVIGAGPGGYTAAFRAADLGMDVTLVERYDSLGGVCLNVGCIPSKALLHTAAVIRETEH 178

Query: 183 LAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVE 242
           +A+HG+ F + +ID + L  +K  VV KLTGGL  MAK RKV    G   F+D H + ++
Sbjct: 179 MASHGVTFSKPEIDREKLLGFKQSVVQKLTGGLGQMAKQRKVNRKTGEAKFIDAHTVTID 238

Query: 243 LTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALELPEVPNKMLV 301
              GE          + F++ IIAAGSQ  KLP +P ED R++DST ALE+ ++P  ML+
Sbjct: 239 ---GE---------TLTFKQCIIAAGSQVFKLPGMPWEDDRLMDSTDALEMQDIPKSMLI 286

Query: 302 IGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTV 361
           IGGGIIGLEMATVYS LG +I +VEM+D ++ GAD+DLVK   +  K ++ ++ LK+K  
Sbjct: 287 IGGGIIGLEMATVYSALGTEITIVEMMDQIIPGADKDLVKPLMQHIKKQYKEIKLKSKVT 346

Query: 362 GVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDK 421
              A   G+ V+F+G    AE   YD VLV+VGR PNGK + AEKAGV V++RGFI VDK
Sbjct: 347 ACVANKTGLEVEFDG----AEKVTYDRVLVAVGRIPNGKLLDAEKAGVEVTDRGFIEVDK 402

Query: 422 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAW 481
           QMRTNV HIFAIGDIVGQPMLAHKA HEA VAAE AHG+K YFDA  IPSVA+TDPEVAW
Sbjct: 403 QMRTNVDHIFAIGDIVGQPMLAHKATHEAKVAAEVAHGQKVYFDALVIPSVAYTDPEVAW 462

Query: 482 AGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAG 541
            GLTE E KE+ + Y  G FPWAASGRAI N R EGFTKL+FD ET+R++G GIVGT+AG
Sbjct: 463 VGLTELEAKEQDLAYEIGKFPWAASGRAIGNDRTEGFTKLLFDPETNRILGAGIVGTNAG 522

Query: 542 DLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           +LISE+CLAIEMG +A DIG TIHPHPTL ES+ M+AE YEGT TD+  P+K+
Sbjct: 523 ELISELCLAIEMGCEAADIGLTIHPHPTLAESVAMSAEAYEGTITDLYLPKKK 575


Lambda     K      H
   0.316    0.134    0.387 

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: 939
Number of extensions: 39
Number of successful extensions: 7
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: 594
Length of database: 575
Length adjustment: 37
Effective length of query: 557
Effective length of database: 538
Effective search space:   299666
Effective search space used:   299666
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: 53 (25.0 bits)

Align candidate WP_099017805.1 CCS90_RS01865 (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.565838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-157  508.8   4.0   9.5e-157  508.3   4.0    1.1  1  NCBI__GCF_002591915.1:WP_099017805.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099017805.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.3   4.0  9.5e-157  9.5e-157       3     456 ..     118     564 ..     116     568 .. 0.98

  Alignments for each domain:
  == domain 1  score: 508.3 bits;  conditional E-value: 9.5e-157
                             TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           +++viG+GpgGY+aA raa lg+ v+lve+ ++lGG+ClnvGCiP+KalL++a v++e ++++++g++ ++ +
  NCBI__GCF_002591915.1:WP_099017805.1 118 ELLVIGAGPGGYTAAFRAADLGMDVTLVERyDSLGGVCLNVGCIPSKALLHTAAVIRETEHMASHGVTFSKPE 190
                                           789***************************9****************************************** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           +d ekll  k++vv+kl+gG+ ++ k+ kv+  +Geak+ d+++v++++e+    l++k++iiA Gs++ +lp
  NCBI__GCF_002591915.1:WP_099017805.1 191 IDREKLLGFKQSVVQKLTGGLGQMAKQRKVNRKTGEAKFIDAHTVTIDGET----LTFKQCIIAAGSQVFKLP 259
                                           ************************************************997....89**************** PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                           + +  + +++++s++ale++ +p+s++i+GgG+iG+E+a++++ lG+++t++e++d+i+p  d+++ k l+++
  NCBI__GCF_002591915.1:WP_099017805.1 260 G-MPWEDDRLMDSTDALEMQDIPKSMLIIGGGIIGLEMATVYSALGTEITIVEMMDQIIPGADKDLVKPLMQH 331
                                           *.7777778**************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                           +kk+  +i+ ++kvt++ +++  ++ve ++   e++++++vLvavGr pn + l+ ek gve+++rg+i+vd+
  NCBI__GCF_002591915.1:WP_099017805.1 332 IKKQYKEIKLKSKVTACVANKTGLEVEFDGA--EKVTYDRVLVAVGRIPNGKLLDAEKAGVEVTDRGFIEVDK 402
                                           ***************************9999..8*************************************** PP

                             TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                           ++rtnv++i+aiGD++g++mLAh+A++e+ vaae + g++   +d+ ++Psv yt+Peva vGlte +ake+ 
  NCBI__GCF_002591915.1:WP_099017805.1 403 QMRTNVDHIFAIGDIVGQPMLAHKATHEAKVAAEVAHGQKV-YFDALVIPSVAYTDPEVAWVGLTELEAKEQD 474
                                           **************************************665.9****************************** PP

                             TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                            ++++gkfp aa+g+a+  + t+Gf k+++d++t++ilGa ivg++a elisel la+e++ ++ ++  tihp
  NCBI__GCF_002591915.1:WP_099017805.1 475 LAYEIGKFPWAASGRAIGNDRTEGFTKLLFDPETNRILGAGIVGTNAGELISELCLAIEMGCEAADIGLTIHP 547
                                           ************************************************************************* PP

                             TIGR01350 440 HPtlsEaikeaalaalg 456
                                           HPtl+E ++ +a+a  g
  NCBI__GCF_002591915.1:WP_099017805.1 548 HPTLAESVAMSAEAYEG 564
                                           *******9998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (575 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: 18.35
//
[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:

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 2024 update 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