Alignments for a candidate for lpd in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas putida KT2440

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PP_5366 PP_5366 dihydrolipoyl dehydrogenase

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__Putida:PP_5366
          Length = 466

 Score =  714 bits (1844), Expect = 0.0
 Identities = 349/465 (75%), Positives = 402/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M+SYDV++IG GPGGYNAAIRAGQLGL VACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MKSYDVVIIGGGPGGYNAAIRAGQLGLSVACVEGRSTLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AASG EFA LGI V P L+LAQMMKQKDESV  LT+G+E+LFRK+KV+WIKGW RL G 
Sbjct: 61  EAASGDEFAHLGIEVKPTLNLAQMMKQKDESVTGLTKGIEYLFRKNKVEWIKGWGRLDGI 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V   DG    L+A+DIVIATGSEP PLPGV VDNQRI+DSTGAL L +VP+HLVVI
Sbjct: 121 GKVVVKAEDGSETALQAKDIVIATGSEPTPLPGVTVDNQRIIDSTGALSLPQVPKHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLG+QVTV+EYL+RICPG D ETA+TLQ+AL +QGM F+LG++V  
Sbjct: 181 GAGVIGLELGSVWRRLGSQVTVIEYLDRICPGTDTETAKTLQKALAKQGMVFKLGSKVTQ 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +G  GV L L+PAAGG  ESLQADYVLVAIGRRPYT+GL LE+VGL +D+RGML N+ 
Sbjct: 241 ATAGADGVSLTLEPAAGGTAESLQADYVLVAIGRRPYTKGLNLESVGLEADKRGMLNNEH 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R++ PGVWVIGDVTSGPMLAHKAE+EA+ CIERIAG   E+N  +IP VIYT+PE+A+V
Sbjct: 301 HRTSVPGVWVIGDVTSGPMLAHKAEDEAVACIERIAGKPHEVNYNLIPGVIYTRPEMATV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  EEQL+A  R YKVG+FPF+ANSRAKINHE+EGF K+++DA +D+VLGVH++GP VSE
Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVIADAETDEVLGVHLVGPSVSE 420

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAM+V G AMQ
Sbjct: 421 MIGEFCVAMEFSASAEDIALTCHPHPTRSEALRQAAMNVDGMAMQ 465


Lambda     K      H
   0.318    0.135    0.390 

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: 782
Number of extensions: 23
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: 467
Length of database: 466
Length adjustment: 33
Effective length of query: 434
Effective length of database: 433
Effective search space:   187922
Effective search space used:   187922
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 PP_5366 PP_5366 (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.32190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.7e-169  549.2   1.9   4.1e-169  549.0   1.9    1.0  1  lcl|FitnessBrowser__Putida:PP_5366  PP_5366 dihydrolipoyl dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5366  PP_5366 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.0   1.9  4.1e-169  4.1e-169       1     459 [.       3     464 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 549.0 bits;  conditional E-value: 4.1e-169
                           TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelgieven 72 
                                         +ydvv+iGgGpgGY aAira+qlgl+va+ve  ++lGGtClnvGC+P+KalL+++e++e ++   +++lgiev +
  lcl|FitnessBrowser__Putida:PP_5366   3 SYDVVIIGGGPGGYNAAIRAGQLGLSVACVEGrSTLGGTCLNVGCMPSKALLHASELYEAASGdeFAHLGIEV-K 76 
                                         59*****************************8799************************99755699****98.7 PP

                           TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprel 146
                                          +l+l++++++k++ v+ l++G+++L++knkve ikG ++l + ++v vk+e+++ + l+ak+i+iAtGsep+ l
  lcl|FitnessBrowser__Putida:PP_5366  77 PTLNLAQMMKQKDESVTGLTKGIEYLFRKNKVEWIKGWGRLDGIGKVVVKAEDGSeTALQAKDIVIATGSEPTPL 151
                                         89*************************************************99886789**************** PP

                           TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221
                                         p+ + +d++++i+s++al+l++vp++lv++G+GviG+E++s++++lG++vtvie+ldri+p +d+e +k+l+k+l
  lcl|FitnessBrowser__Putida:PP_5366 152 PG-VTVDNQRIIDSTGALSLPQVPKHLVVIGAGVIGLELGSVWRRLGSQVTVIEYLDRICPGTDTETAKTLQKAL 225
                                         **.9999999***************************************************************** PP

                           TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                          k+g+ ++ ++kvt+ ++ +d v+  +e   + ++e+l+a++vLva+Gr+p +++l+le++g+e d+rg+++ +e
  lcl|FitnessBrowser__Putida:PP_5366 226 AKQGMVFKLGSKVTQATAGADGVSltLEPAAGgTAESLQADYVLVAIGRRPYTKGLNLESVGLEADKRGMLN-NE 299
                                         *********************99955444444589**********************************665.99 PP

                           TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegie 368
                                         + rt+vpg+++iGDv++++mLAh+A++e+v ++e+iagk + e++y+++P viyt+Pe+a+vG+teeq+k+eg +
  lcl|FitnessBrowser__Putida:PP_5366 300 HHRTSVPGVWVIGDVTSGPMLAHKAEDEAVACIERIAGKPH-EVNYNLIPGVIYTRPEMATVGKTEEQLKAEGRA 373
                                         **************************************776.9******************************** PP

                           TIGR01350 369 vkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtl 443
                                         +kvgkfpf+an++a + +et+Gf+kvi+d +t+e+lG+h+vg+++se+i e+ +a+e+ +++e++a t+hpHPt 
  lcl|FitnessBrowser__Putida:PP_5366 374 YKVGKFPFTANSRAKINHETEGFAKVIADAETDEVLGVHLVGPSVSEMIGEFCVAMEFSASAEDIALTCHPHPTR 448
                                         *************************************************************************** PP

                           TIGR01350 444 sEaikeaalaalgkai 459
                                         sEa+ +aa ++ g+a+
  lcl|FitnessBrowser__Putida:PP_5366 449 SEALRQAAMNVDGMAM 464
                                         *********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.08
//
[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