Alignments for a candidate for fba in Sulfurimonas denitrificans DSM 1251

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Sulfurimonas denitrificans DSM 1251

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011372143.1 SUDEN_RS02660 class II fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>NCBI__GCF_000012965.1:WP_011372143.1
          Length = 357

 Score =  518 bits (1335), Expect = e-152
 Identities = 250/354 (70%), Positives = 295/354 (83%), Gaps = 1/354 (0%)

Query: 4   IFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSN 63
           I D VK GV+ GDDV+KV+Q AKEN FA+PA+N VGTDSINA+LE AAKVK+PVI+QFSN
Sbjct: 3   ILDIVKAGVLFGDDVKKVYQHAKENGFAIPAINVVGTDSINAILEAAAKVKSPVIIQFSN 62

Query: 64  GGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGL 123
           GGASF AGKG+ +D  + AAI GA+SGA HVH MA  YGVPVILHTDH AKKLLPW+D L
Sbjct: 63  GGASFYAGKGLSND-GEKAAIAGAVSGAIHVHMMALSYGVPVILHTDHAAKKLLPWVDAL 121

Query: 124 LDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEE 183
           L+  EK++    +PL+SSHM+DLSEESLQENI I  KYL+RMSKIG+++EIELG TGGEE
Sbjct: 122 LEESEKYYKTHARPLYSSHMLDLSEESLQENISISKKYLQRMSKIGISIEIELGVTGGEE 181

Query: 184 DGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILR 243
           DGVDNS +D S LYTQPEDV YAY ELS++SP FTIAASFGNVHGVYKPGNVVLTP IL 
Sbjct: 182 DGVDNSSVDNSLLYTQPEDVAYAYKELSEVSPNFTIAASFGNVHGVYKPGNVVLTPKILD 241

Query: 244 DSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNY 303
           +SQ+Y+ +K       +NFVFHGGSGS+ QEI++++SYGVVKMNIDTDTQWATW GV  Y
Sbjct: 242 NSQKYIQEKFKTEQKPVNFVFHGGSGSSLQEIREAISYGVVKMNIDTDTQWATWVGVKEY 301

Query: 304 YKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAID 357
           Y+ N  YLQGQ+GNP+GED+PNK YYDPR WLR GQ ++I R+E+AF +LNAID
Sbjct: 302 YEKNRDYLQGQIGNPEGEDKPNKNYYDPRKWLRDGQKTLIKRVEEAFSDLNAID 355


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: 489
Number of extensions: 13
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: 357
Length adjustment: 29
Effective length of query: 330
Effective length of database: 328
Effective search space:   108240
Effective search space used:   108240
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 WP_011372143.1 SUDEN_RS02660 (class II fructose-bisphosphate aldolase)
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.30022.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-179  581.3   1.7   3.8e-179  581.2   1.7    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011372143.1  SUDEN_RS02660 class II fructose-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011372143.1  SUDEN_RS02660 class II fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.2   1.7  3.8e-179  3.8e-179       1     356 [.       3     356 ..       3     357 .] 0.99

  Alignments for each domain:
  == domain 1  score: 581.2 bits;  conditional E-value: 3.8e-179
                                 TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGk 69 
                                               +ld++k+gv  g+dv+k+++ ake+ faiPainvv+++++na+leaa+++ksp+i+qfsngga+f+aGk
  lcl|NCBI__GCF_000012965.1:WP_011372143.1   3 ILDIVKAGVLFGDDVKKVYQHAKENGFAIPAINVVGTDSINAILEAAAKVKSPVIIQFSNGGASFYAGK 71 
                                               6799***************************************************************** PP

                                 TIGR01520  70 GvkdeaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfss 138
                                               G++++ eka +iaGa+++a +v+++a  ygvpv+lhtdh akkllp+vd+lle++eky+k + +Pl+ss
  lcl|NCBI__GCF_000012965.1:WP_011372143.1  72 GLSNDGEKA-AIAGAVSGAIHVHMMALSYGVPVILHTDHAAKKLLPWVDALLEESEKYYKTHARPLYSS 139
                                               ********9.9********************************************************** PP

                                 TIGR01520 139 hmldlseepieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeel 207
                                               hmldlsee+++eni+i+kkyl+rm+ki + +eie+G+tGGeedGvdn+++d++ lyt+Pedv ++y+el
  lcl|NCBI__GCF_000012965.1:WP_011372143.1 140 HMLDLSEESLQENISISKKYLQRMSKIGISIEIELGVTGGEEDGVDNSSVDNSLLYTQPEDVAYAYKEL 208
                                               ********************************************************************* PP

                                 TIGR01520 208 skispkfsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikea 276
                                               s++sp+f+iaa+fGnvhGvykpGnv+l+P+il ++q+y++ek  ++ +kp++fvfhGGsGs+ +ei+ea
  lcl|NCBI__GCF_000012965.1:WP_011372143.1 209 SEVSPNFTIAASFGNVHGVYKPGNVVLTPKILDNSQKYIQEKFKTE-QKPVNFVFHGGSGSSLQEIREA 276
                                               *******************************************998.9********************* PP

                                 TIGR01520 277 lsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarve 345
                                               +syGvvk+n+dtdtq+a+++g+++y+ kn+dylq+q+Gnp+ge+kpnk +ydPr wlr+++k++++rve
  lcl|NCBI__GCF_000012965.1:WP_011372143.1 277 ISYGVVKMNIDTDTQWATWVGVKEYYEKNRDYLQGQIGNPEGEDKPNKNYYDPRKWLRDGQKTLIKRVE 345
                                               ********************************************************************* PP

                                 TIGR01520 346 kaleelnaink 356
                                               +a+ +lnai++
  lcl|NCBI__GCF_000012965.1:WP_011372143.1 346 EAFSDLNAIDR 356
                                               ********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (357 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.09
//
[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