GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Rhodococcus qingshengii djl-6-2

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_007734084.1 C1M55_RS04085 4-hydroxy-2-oxovalerate aldolase

Query= BRENDA::P9WMK5
         (346 letters)



>NCBI__GCF_002893965.1:WP_007734084.1
          Length = 347

 Score =  567 bits (1460), Expect = e-166
 Identities = 285/333 (85%), Positives = 303/333 (90%)

Query: 5   WDVRITDTSLRDGSHHKRHQFTKDEVGAIVAALDAAGVPVIEVTHGDGLGGSSFNYGFSK 64
           WD+R+TDTSLRDGSHHKRHQFT DEV AIV ALD AGVPVIEVTHGDGLGGSSFNYGFSK
Sbjct: 11  WDIRVTDTSLRDGSHHKRHQFTVDEVRAIVGALDGAGVPVIEVTHGDGLGGSSFNYGFSK 70

Query: 65  TPEQELIKLAAATAKEARIAFLMLPGVGTKDDIKEARDNGGSICRIATHCTEADVSIQHF 124
           TPEQELIK A  TA  A+IAFLMLPG+G KDDI  A+DNG SICRIATHCTEADVSIQHF
Sbjct: 71  TPEQELIKAAVETATNAKIAFLMLPGLGIKDDIVIAQDNGASICRIATHCTEADVSIQHF 130

Query: 125 GLARELGLETVGFLMMAHTIAPEKLAAQARIMADAGCQCVYVVDSAGALVLDGVADRVSA 184
           GLARE GLETVGFLMMAH+I PEKLA QARIMADAGCQCVYVVDSAGALVL+ V+DRV A
Sbjct: 131 GLARERGLETVGFLMMAHSIPPEKLAKQARIMADAGCQCVYVVDSAGALVLEQVSDRVEA 190

Query: 185 LVAELGEDAQVGFHGHENLGLGVANSVAAVRAGAKQIDGSCRRFGAGAGNAPVEALIGVF 244
           LV ELG DAQVGFHGHENLGLGVANS+AAVRAGAKQIDGS RRFGAGAGNAPVEA +GV 
Sbjct: 191 LVQELGNDAQVGFHGHENLGLGVANSIAAVRAGAKQIDGSTRRFGAGAGNAPVEAFVGVC 250

Query: 245 DKIGVKTGIDFFDIADAAEDVVRPAMPAECLLDRNALIMGYSGVYSSFLKHAVRQAERYG 304
           DKIGVKTGIDFF IADAAEDVVRPAMP ECLLDR AL+MGY+GVYSSFLKHA RQAERYG
Sbjct: 251 DKIGVKTGIDFFAIADAAEDVVRPAMPQECLLDRQALMMGYAGVYSSFLKHAERQAERYG 310

Query: 305 VPASALLHRAGQRKLIGGQEDQLIDIALEIKRE 337
           V ++ LL RAG+RKL+GGQEDQLIDIALE++RE
Sbjct: 311 VSSAELLVRAGKRKLVGGQEDQLIDIALELQRE 343


Lambda     K      H
   0.320    0.136    0.393 

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: 495
Number of extensions: 17
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: 346
Length of database: 347
Length adjustment: 29
Effective length of query: 317
Effective length of database: 318
Effective search space:   100806
Effective search space used:   100806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_007734084.1 C1M55_RS04085 (4-hydroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

# 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/TIGR03217.hmm
# target sequence database:        /tmp/gapView.2719779.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03217  [M=334]
Accession:   TIGR03217
Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-162  524.0   5.5   9.3e-162  523.8   5.5    1.0  1  NCBI__GCF_002893965.1:WP_007734084.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_007734084.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.8   5.5  9.3e-162  9.3e-162       3     333 ..      13     343 ..      11     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.8 bits;  conditional E-value: 9.3e-162
                             TIGR03217   3 ltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeavk 75 
                                           +++td++LrdGsh++rhqft++evrai+ aLd agv++iev+hGdGLggss+nyGfs++ ++eli+aa+e+++
  NCBI__GCF_002893965.1:WP_007734084.1  13 IRVTDTSLRDGSHHKRHQFTVDEVRAIVGALDGAGVPVIEVTHGDGLGGSSFNYGFSKTPEQELIKAAVETAT 85 
                                           89*********************************************************************** PP

                             TIGR03217  76 kakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklaeq 148
                                           +ak+a l+lPG+g ++++  a+d+G++++r+athcteadvs qh++lare gletvgfLmm+h+++pekla+q
  NCBI__GCF_002893965.1:WP_007734084.1  86 NAKIAFLMLPGLGIKDDIVIAQDNGASICRIATHCTEADVSIQHFGLARERGLETVGFLMMAHSIPPEKLAKQ 158
                                           ************************************************************************* PP

                             TIGR03217 149 akllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridasl 221
                                           a+++ + G+++vyvvdsaGal++e+v+drv+al ++l ++++vG+h+henl+l+vansi+av++Ga++id+s 
  NCBI__GCF_002893965.1:WP_007734084.1 159 ARIMADAGCQCVYVVDSAGALVLEQVSDRVEALVQELGNDAQVGFHGHENLGLGVANSIAAVRAGAKQIDGST 231
                                           ************************************************************************* PP

                             TIGR03217 222 aglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhaer 294
                                           +++GagaGnap+e++v+v+d++G++tg+d+f+++daaedvvrP +++++ +dr+al++GyaGvyssfl+haer
  NCBI__GCF_002893965.1:WP_007734084.1 232 RRFGAGAGNAPVEAFVGVCDKIGVKTGIDFFAIADAAEDVVRPAMPQECLLDRQALMMGYAGVYSSFLKHAER 304
                                           ************************************************************************* PP

                             TIGR03217 295 aaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                           +ae+ygv+++++lv+ G+rklvgGqed+++d+al+l++e
  NCBI__GCF_002893965.1:WP_007734084.1 305 QAERYGVSSAELLVRAGKRKLVGGQEDQLIDIALELQRE 343
                                           ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (347 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: 00:00:00.00
# Mc/sec: 13.03
//
[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:

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:

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:

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:

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