GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Echinicola vietnamensis KMM 6221, DSM 17526

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate Echvi_2849 Echvi_2849 fructose-bisphosphate aldolase, class II, yeast/E. coli subtype

Query= BRENDA::P0AB71
         (359 letters)



>FitnessBrowser__Cola:Echvi_2849
          Length = 353

 Score =  464 bits (1193), Expect = e-135
 Identities = 223/349 (63%), Positives = 276/349 (79%), Gaps = 1/349 (0%)

Query: 9   KPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASF 68
           KPG+  G++++ + + AKE+ FALPAVN + T + NAVLETA KV +PVIVQFSNGGA F
Sbjct: 4   KPGIKFGEELKDLLEYAKESEFALPAVNVINTSTANAVLETAKKVNSPVIVQFSNGGAQF 63

Query: 69  IAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGE 128
            AGKG+ +D  Q A+I GA+SGA HVH+MAE YGVPVILHTDH AKKL+PW+DG+L+AG+
Sbjct: 64  FAGKGLANDKQQ-ASIAGAVSGAMHVHKMAEAYGVPVILHTDHAAKKLIPWVDGMLEAGK 122

Query: 129 KHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVDN 188
           +++AA  KPLFSSHM+DLSEE ++ENIE   KYL    K+ M LEIELG TGGEEDGVDN
Sbjct: 123 EYYAAFKKPLFSSHMLDLSEEPIEENIETSVKYLAEFKKLEMALEIELGVTGGEEDGVDN 182

Query: 189 SHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQEY 248
           + +D+S LYTQPE+V YAY +L + S  FTIAA+FGNVHGVYKPGNV L P IL++SQ+Y
Sbjct: 183 TDIDSSKLYTQPEEVAYAYEKLREQSELFTIAAAFGNVHGVYKPGNVSLQPKILKNSQDY 242

Query: 249 VSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANE 308
           + +K  L    ++FVFHGGSGS+ +EI+++  YG +KMNIDTD QWA WEGVL YYK NE
Sbjct: 243 ICEKFGLSGKPVSFVFHGGSGSSVEEIREATGYGSIKMNIDTDMQWAFWEGVLKYYKENE 302

Query: 309 AYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAID 357
            YLQ QLGNP+G D PNKK YDPRVWLR G+ + + RLE AF  LNA+D
Sbjct: 303 GYLQTQLGNPEGPDVPNKKKYDPRVWLRKGEENFVKRLEVAFDMLNAVD 351


Lambda     K      H
   0.316    0.133    0.392 

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: 443
Number of extensions: 11
Number of successful extensions: 2
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: 359
Length of database: 353
Length adjustment: 29
Effective length of query: 330
Effective length of database: 324
Effective search space:   106920
Effective search space used:   106920
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: 49 (23.5 bits)

Align candidate Echvi_2849 Echvi_2849 (fructose-bisphosphate aldolase, class II, yeast/E. coli subtype)
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))

# 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/TIGR01520.hmm
# target sequence database:        /tmp/gapView.9844.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.3e-169  549.0   0.6   2.6e-169  548.8   0.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2849  Echvi_2849 fructose-bisphosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2849  Echvi_2849 fructose-bisphosphate aldolase, class II, yeast/E. coli subtype
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.8   0.6  2.6e-169  2.6e-169       5     356 ..       3     352 ..       1     353 [] 0.99

  Alignments for each domain:
  == domain 1  score: 548.8 bits;  conditional E-value: 2.6e-169
                            TIGR01520   5 lktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaeka 78 
                                           k+g+  ge++++l+e+ake +fa+Pa+nv+ ++t+na+le+a++++sp+i+qfsngga+f+aGkG+ +++++a
  lcl|FitnessBrowser__Cola:Echvi_2849   3 FKPGIKFGEELKDLLEYAKESEFALPAVNVINTSTANAVLETAKKVNSPVIVQFSNGGAQFFAGKGLANDKQQA 76 
                                          689********************************************************************999 PP

                            TIGR01520  79 asiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlseepieeni 152
                                           siaGa+++a++v+++ae+ygvpv+lhtdh akkl+p+vdg+lea+++y+++ +kPlfsshmldlseepieeni
  lcl|FitnessBrowser__Cola:Echvi_2849  77 -SIAGAVSGAMHVHKMAEAYGVPVILHTDHAAKKLIPWVDGMLEAGKEYYAAFKKPLFSSHMLDLSEEPIEENI 149
                                          .************************************************************************* PP

                            TIGR01520 153 eiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafGnvhGv 226
                                          e+++kyl    k+++ leie+G+tGGeedGvdn + d+++lyt+Pe+v ++ye+l++ s  f+iaaafGnvhGv
  lcl|FitnessBrowser__Cola:Echvi_2849 150 ETSVKYLAEFKKLEMALEIELGVTGGEEDGVDNTDIDSSKLYTQPEEVAYAYEKLREQSELFTIAAAFGNVHGV 223
                                          ************************************************************************** PP

                            TIGR01520 227 ykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaalegild 300
                                          ykpGnv l+P+il+++q+y+ ek gl   kp+sfvfhGGsGs++eei+ea  yG +k+n+dtd+q+a++eg+l+
  lcl|FitnessBrowser__Cola:Echvi_2849 224 YKPGNVSLQPKILKNSQDYICEKFGLS-GKPVSFVFHGGSGSSVEEIREATGYGSIKMNIDTDMQWAFWEGVLK 296
                                          **************************9.9********************************************* PP

                            TIGR01520 301 yvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                          y+++ne ylq+q+Gnp+g+++pnkk+ydPrvwlr++e+   +r+e a++ lna+++
  lcl|FitnessBrowser__Cola:Echvi_2849 297 YYKENEGYLQTQLGNPEGPDVPNKKKYDPRVWLRKGEENFVKRLEVAFDMLNAVDR 352
                                          ****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (353 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: 7.06
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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