Alignments for a candidate for lpd in Aquimarina macrocephali JAMB N27

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Aquimarina macrocephali JAMB N27

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_024770448.1 Z054_RS0112740 dihydrolipoyl dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>NCBI__GCF_000520995.1:WP_024770448.1
          Length = 468

 Score =  458 bits (1179), Expect = e-133
 Identities = 233/465 (50%), Positives = 319/465 (68%), Gaps = 3/465 (0%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           DV +IG GPGGYVAAI+ AQLG+KT  IEK   LGGTCLNVGCIPSKALL SSH Y  A 
Sbjct: 5   DVAVIGSGPGGYVAAIRCAQLGMKTAIIEKYSTLGGTCLNVGCIPSKALLDSSHHYEHAV 64

Query: 105 HVFANHGVKV-SSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEV 163
             FA+HG+++   V+++L  M+A+K + V     GV  L KKNK++  +G G F   + V
Sbjct: 65  KHFADHGIEIPGDVKINLEKMIARKQSVVDQTCDGVSFLMKKNKIDVFEGVGSFKDATHV 124

Query: 164 SVDTIDGENVVVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLTEIPKKLIVIGAG 223
           ++   DG    ++ K+ I+ATGS   +LP I ID+K++++ST AL L E+PK LI+IG G
Sbjct: 125 NITKADGTVETIEAKNTIIATGSKPSTLPFIKIDKKRVITSTEALKLKEVPKHLIIIGGG 184

Query: 224 YIGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVDS 283
            IGLE+G V+ RLG+EV+VVE+   I+P MD  + K+ Q+ ++KQK K     KV GV  
Sbjct: 185 VIGLELGQVYRRLGAEVSVVEYMDRIIPGMDKALSKELQKVMKKQKSKIYTSHKVTGVSV 244

Query: 284 SGDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERFS 343
           SGD V +  +  +G     L+ D  LVS GR P+T GL+ E  GV+ +  G++ VN+   
Sbjct: 245 SGDEVTVTADDKKGNP-VELKGDYCLVSVGRRPYTDGLNAEAAGVKLNDRGQVEVNDHLQ 303

Query: 344 TNVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVGK 403
           T+ S +YAIGDVI G MLAHKAEE+G    E +AG+  H+DY+ +PGVVYT+PEVA+VGK
Sbjct: 304 TSASNIYAIGDVIKGAMLAHKAEEEGTFVAETLAGQKPHIDYNLIPGVVYTWPEVAAVGK 363

Query: 404 TEEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGELI 463
           TEE+L + G+ Y  G+FPF A  R++A    +G VKILAD+ TD++LGVH++     +LI
Sbjct: 364 TEEELTEAGIKYKSGQFPFRALGRSRASGDLDGFVKILADETTDEVLGVHMIGARCADLI 423

Query: 464 HEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYD-KPIHM 507
            EAV A+ + AS+EDI+R+ HAHPT +EA+KEAA+A  D + +HM
Sbjct: 424 AEAVTAMEFRASAEDISRMSHAHPTFTEAVKEAALAATDNRALHM 468


Lambda     K      H
   0.315    0.134    0.376 

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: 575
Number of extensions: 26
Number of successful extensions: 3
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: 507
Length of database: 468
Length adjustment: 34
Effective length of query: 473
Effective length of database: 434
Effective search space:   205282
Effective search space used:   205282
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: 52 (24.6 bits)

Align candidate WP_024770448.1 Z054_RS0112740 (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.3567638.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-178  579.6   9.9   2.4e-178  579.5   9.9    1.0  1  NCBI__GCF_000520995.1:WP_024770448.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000520995.1:WP_024770448.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.5   9.9  2.4e-178  2.4e-178       2     457 ..       4     463 ..       3     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 579.5 bits;  conditional E-value: 2.4e-178
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevvee.lkeakelgieven 72 
                                           ydv viG+GpgGYvaAir+aqlg+k+a++ek ++lGGtClnvGCiP+KalL s++ +e+ +k+++++gie+ +
  NCBI__GCF_000520995.1:WP_024770448.1   4 YDVAVIGSGPGGYVAAIRCAQLGMKTAIIEKySTLGGTCLNVGCIPSKALLDSSHHYEHaVKHFADHGIEIPG 76 
                                           9******************************99***********************9871566********99 PP

                             TIGR01350  73 .vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                            vk++lek+ +rk++vv++  +Gv++L+kknk++v++G ++++d+++v+++k +++ +++eakn iiAtGs+p
  NCBI__GCF_000520995.1:WP_024770448.1  77 dVKINLEKMIARKQSVVDQTCDGVSFLMKKNKIDVFEGVGSFKDATHVNITKADGTvETIEAKNTIIATGSKP 149
                                           9****************************************************9999**************** PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                           ++lp+ ++ d+k+vits+eal+lkevp++l+i+GgGviG+E+++++++lG++v+v+e++dri+p +d+ +sk+
  NCBI__GCF_000520995.1:WP_024770448.1 150 STLPF-IKIDKKRVITSTEALKLKEVPKHLIIIGGGVIGLELGQVYRRLGAEVSVVEYMDRIIPGMDKALSKE 221
                                           *****.9****************************************************************** PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           l+k +kk++ ki+t++kvt v+ + dev+v+a++k  +  +l++++ Lv+vGr+p +++l+ e+ gv+l++rg
  NCBI__GCF_000520995.1:WP_024770448.1 222 LQKVMKKQKSKIYTSHKVTGVSVSGDEVTVTADDKkgNPVELKGDYCLVSVGRRPYTDGLNAEAAGVKLNDRG 294
                                           *******************99999999996665553577899******************************* PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           +++v+++l+t++++iyaiGDvi+++mLAh+A++eg+ +ae++ag+++ +idy+++P v+yt Peva+vG+tee
  NCBI__GCF_000520995.1:WP_024770448.1 295 QVEVNDHLQTSASNIYAIGDVIKGAMLAHKAEEEGTFVAETLAGQKP-HIDYNLIPGVVYTWPEVAAVGKTEE 366
                                           ********************************************998.9************************ PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           ++ e+gi++k+g+fpf+a g+++a+++ dGfvk+++d++t+e+lG+h++ga+ ++li+e++ a+e+++++e++
  NCBI__GCF_000520995.1:WP_024770448.1 367 ELTEAGIKYKSGQFPFRALGRSRASGDLDGFVKILADETTDEVLGVHMIGARCADLIAEAVTAMEFRASAEDI 439
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgk 457
                                           +++ h+HPt++Ea+keaalaa+++
  NCBI__GCF_000520995.1:WP_024770448.1 440 SRMSHAHPTFTEAVKEAALAATDN 463
                                           ******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.58
//
[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 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