Alignments for a candidate for lpd in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Azospirillum sp. B510

Align Dihydrolipoyl dehydrogenase 1, mitochondrial; AtmLPD1; mtLPD1; Dihydrolipoamide dehydrogenase 1; Glycine cleavage system L protein 1; Pyruvate dehydrogenase complex E3 subunit 1; E3-1; PDC-E3 1; EC 1.8.1.4 (characterized)
to candidate WP_042443139.1 AZL_RS13320 dihydrolipoyl dehydrogenase

Query= SwissProt::Q9M5K3
         (507 letters)



>NCBI__GCF_000010725.1:WP_042443139.1
          Length = 465

 Score =  567 bits (1460), Expect = e-166
 Identities = 285/463 (61%), Positives = 347/463 (74%), Gaps = 4/463 (0%)

Query: 45  DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           DVV+IGGGPGGYV AI+A+QLG K  C+EKRG LGGTCLNVGCIPSKALL +S  + EA 
Sbjct: 7   DVVVIGGGPGGYVCAIRAAQLGFKVACVEKRGTLGGTCLNVGCIPSKALLAASEKFEEAA 66

Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164
           H  A  GIKV  VE+DLP M A KD  VK+   GIE LFKKNKVT++KG GK  + N V 
Sbjct: 67  HGLAKFGIKVGGVELDLPGMQAHKDKVVKDNVTGIEFLFKKNKVTWLKGAGKITAANTVE 126

Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLSEVPKKLIVIGAGY 224
           VE   G   I   K I++ATGSDV  LPGI IDE ++VSSTGALSL EVPK L+VIG G 
Sbjct: 127 VE---GVGAITASKAIVIATGSDVAPLPGIAIDETRVVSSTGALSLPEVPKHLVVIGGGV 183

Query: 225 IGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVDSS 284
           IGLE+GSVWGRLG++VTVVE+   ++P+MDGE+ KQ QR   KQ M F L TKV     +
Sbjct: 184 IGLELGSVWGRLGAKVTVVEYLDRVLPTMDGELSKQAQRIFAKQGMDFKLSTKVTGAAVT 243

Query: 285 SDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRFLS 344
             GV LTVEPA GGE   +EAD VLV+ GR P+T GL LE +GVE ++ GR+ ++  F +
Sbjct: 244 EAGVTLTVEPAAGGEAQTIEADTVLVAIGRRPYTEGLGLEAVGVELER-GRVKIDGHFQT 302

Query: 345 NVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVGKT 404
           NVPG+YAIGDV+ GPMLAHKAEE+GVA  E +AG+  HV++D VPGVVYT PEVA+VGKT
Sbjct: 303 NVPGIYAIGDVVEGPMLAHKAEEEGVALAEQLAGQKSHVNHDLVPGVVYTWPEVAAVGKT 362

Query: 405 EEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGELIH 464
           EEQLK  GV+Y+ GKFPF AN RA+A  N +G VKIL+D  TD++LGVH++ PN  E+I 
Sbjct: 363 EEQLKAAGVAYKTGKFPFTANGRARAGGNTDGFVKILSDAATDQVLGVHMIGPNVSEMIG 422

Query: 465 EAVLAINYDASSEDIARVCHAHPTMSEALKEAAMATYDKPIHI 507
           E VLA+ + AS+ED+AR CHAHPT+SEA+KEAA+A   + +HI
Sbjct: 423 ELVLAMEFSASAEDVARTCHAHPTLSEAVKEAALAADGRALHI 465


Lambda     K      H
   0.315    0.133    0.375 

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: 665
Number of extensions: 23
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: 465
Length adjustment: 34
Effective length of query: 473
Effective length of database: 431
Effective search space:   203863
Effective search space used:   203863
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate WP_042443139.1 AZL_RS13320 (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.3240668.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-181  587.9  11.3   7.3e-181  587.8  11.3    1.0  1  NCBI__GCF_000010725.1:WP_042443139.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010725.1:WP_042443139.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.8  11.3  7.3e-181  7.3e-181       2     461 .]       6     465 .]       5     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: 587.8 bits;  conditional E-value: 7.3e-181
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 
                                           +dvvviGgGpgGYv+Airaaqlg+kva+vek  +lGGtClnvGCiP+KalL+++e +ee+ + ++++gi+v +
  NCBI__GCF_000010725.1:WP_042443139.1   6 FDVVVIGGGPGGYVCAIRAAQLGFKVACVEKrGTLGGTCLNVGCIPSKALLAASEKFEEAAHgLAKFGIKVGG 78 
                                           8******************************889*************************************** PP

                             TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsepre 145
                                           v+ldl  ++++k+kvvk  v+G+++L+kknkv+ +kG +k++ +++vev++         k+i+iAtGs+++ 
  NCBI__GCF_000010725.1:WP_042443139.1  79 VELDLPGMQAHKDKVVKDNVTGIEFLFKKNKVTWLKGAGKITAANTVEVEGVG--AITASKAIVIATGSDVAP 149
                                           ***************************************************98..4688999*********** PP

                             TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218
                                           lp+ ++ de++v++s++al+l+evp++lv++GgGviG+E++s++ +lG+kvtv+e+ldr+lp++d e+sk+++
  NCBI__GCF_000010725.1:WP_042443139.1 150 LPG-IAIDETRVVSSTGALSLPEVPKHLVVIGGGVIGLELGSVWGRLGAKVTVVEYLDRVLPTMDGELSKQAQ 221
                                           ***.9999999************************************************************** PP

                             TIGR01350 219 kklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelderga 288
                                           + + k+g++++ ++kvt    +e+ v+  ve   + e++t+ea+ vLva+Gr+p +e+lgle++gvel++ g+
  NCBI__GCF_000010725.1:WP_042443139.1 222 RIFAKQGMDFKLSTKVTGAAVTEAGVTltVEPAAGgEAQTIEADTVLVAIGRRPYTEGLGLEAVGVELER-GR 293
                                           *****************66666666654477666669******************************988.** PP

                             TIGR01350 289 ikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeq 361
                                           +k+d +++tnvpgiyaiGDv++++mLAh+A++egv  ae++ag+++ ++++++vP v+yt Peva+vG+teeq
  NCBI__GCF_000010725.1:WP_042443139.1 294 VKIDGHFQTNVPGIYAIGDVVEGPMLAHKAEEEGVALAEQLAGQKS-HVNHDLVPGVVYTWPEVAAVGKTEEQ 365
                                           *******************************************776.9************************* PP

                             TIGR01350 362 akeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434
                                           +k++g+++k+gkfpf+ang+a+a ++tdGfvk++ d  t+++lG+h++g+++se+i el+la+e+ +++e++a
  NCBI__GCF_000010725.1:WP_042443139.1 366 LKAAGVAYKTGKFPFTANGRARAGGNTDGFVKILSDAATDQVLGVHMIGPNVSEMIGELVLAMEFSASAEDVA 438
                                           ************************************************************************* PP

                             TIGR01350 435 ktihpHPtlsEaikeaalaalgkaihv 461
                                           +t+h+HPtlsEa+keaalaa g+a+h+
  NCBI__GCF_000010725.1:WP_042443139.1 439 RTCHAHPTLSEAVKEAALAADGRALHI 465
                                           ***********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 00:00:00.00
# Mc/sec: 22.21
//
[ok]

This GapMind analysis is from Apr 09 2024. 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