Alignments for a candidate for fba in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Flavobacterium beibuense F44-8

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_035133950.1 Q763_RS10370 class II fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>NCBI__GCF_000769915.1:WP_035133950.1
          Length = 355

 Score =  499 bits (1285), Expect = e-146
 Identities = 240/352 (68%), Positives = 292/352 (82%), Gaps = 1/352 (0%)

Query: 8   VKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGAS 67
           +KPGV TGD VQ++FQ AKE  FALPAVN  G+ +IN VLETAAK+ APVI+QFSNGG+S
Sbjct: 5   IKPGVATGDQVQEIFQYAKEKGFALPAVNVTGSSTINGVLETAAKLNAPVIIQFSNGGSS 64

Query: 68  FIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAG 127
           + AGKG+ +D  Q +AILGAI+GA H+H +AE YG  VILHTDHCAK LLPWIDGLLDA 
Sbjct: 65  YNAGKGLSND-GQKSAILGAIAGAKHIHTLAEAYGATVILHTDHCAKNLLPWIDGLLDAS 123

Query: 128 EKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVD 187
           E+HF ATGKPLFSSHMIDLSEE L+ENIEI  KYLERMSK+GMTLEIELG TGGEEDGVD
Sbjct: 124 EEHFKATGKPLFSSHMIDLSEEPLEENIEISKKYLERMSKMGMTLEIELGITGGEEDGVD 183

Query: 188 NSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQE 247
           NS +D+S LYTQPE+V YAY ELSK+S RFT+AA+FGNVHGVYKPGNV LTP IL++SQ+
Sbjct: 184 NSDVDSSKLYTQPEEVAYAYEELSKVSNRFTVAAAFGNVHGVYKPGNVKLTPKILKNSQD 243

Query: 248 YVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKAN 307
           Y+ +K+N   N ++FVFHGGSGST +EI+++++YGV+KMNIDTD Q+A  EG+ +Y   N
Sbjct: 244 YIQEKYNTGVNPVDFVFHGGSGSTLEEIREAITYGVIKMNIDTDLQFAFTEGIRDYVSKN 303

Query: 308 EAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359
             YL+ Q+GNP+G D PNKKYYDPR W+R G+ +  ARL KAF++LN ++ L
Sbjct: 304 IEYLKTQIGNPEGADSPNKKYYDPRKWMREGELTFNARLAKAFEDLNNVNTL 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: 480
Number of extensions: 12
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: 355
Length adjustment: 29
Effective length of query: 330
Effective length of database: 326
Effective search space:   107580
Effective search space used:   107580
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_035133950.1 Q763_RS10370 (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.3066401.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-178  578.5   1.0   2.8e-178  578.3   1.0    1.0  1  NCBI__GCF_000769915.1:WP_035133950.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035133950.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.3   1.0  2.8e-178  2.8e-178       3     356 ..       3     354 ..       1     355 [] 0.99

  Alignments for each domain:
  == domain 1  score: 578.3 bits;  conditional E-value: 2.8e-178
                             TIGR01520   3 dklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdea 75 
                                           + +k+gv++g++v+++f++ake+ fa+Pa+nv++s+t+n +le+a++ ++p+i+qfsngg+++ aGkG++++ 
  NCBI__GCF_000769915.1:WP_035133950.1   3 HNIKPGVATGDQVQEIFQYAKEKGFALPAVNVTGSSTINGVLETAAKLNAPVIIQFSNGGSSYNAGKGLSNDG 75 
                                           5789********************************************************************9 PP

                             TIGR01520  76 ekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlseepi 148
                                           +k+ +i Gaia+a++++++ae+yg  v+lhtdhCak+llp++dgll+a+e++fk++gkPlfsshm+dlseep+
  NCBI__GCF_000769915.1:WP_035133950.1  76 QKS-AILGAIAGAKHIHTLAEAYGATVILHTDHCAKNLLPWIDGLLDASEEHFKATGKPLFSSHMIDLSEEPL 147
                                           999.9******************************************************************** PP

                             TIGR01520 149 eenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafG 221
                                           eeniei+kkyl+rm+k+ ++leie+GitGGeedGvdn+++d+++lyt+Pe+v ++yeelsk+s +f++aaafG
  NCBI__GCF_000769915.1:WP_035133950.1 148 EENIEISKKYLERMSKMGMTLEIELGITGGEEDGVDNSDVDSSKLYTQPEEVAYAYEELSKVSNRFTVAAAFG 220
                                           ************************************************************************* PP

                             TIGR01520 222 nvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaa 294
                                           nvhGvykpGnvkl+P+il+++q+y++ek ++   +p++fvfhGGsGst eei+ea++yGv+k+n+dtd+q+a+
  NCBI__GCF_000769915.1:WP_035133950.1 221 NVHGVYKPGNVKLTPKILKNSQDYIQEKYNTG-VNPVDFVFHGGSGSTLEEIREAITYGVIKMNIDTDLQFAF 292
                                           *****************************998.89************************************** PP

                             TIGR01520 295 legildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                           +egi+dyv kn++yl++q+Gnp+g + pnkk+ydPr w+re+e + +ar+ ka+e+ln++n+
  NCBI__GCF_000769915.1:WP_035133950.1 293 TEGIRDYVSKNIEYLKTQIGNPEGADSPNKKYYDPRKWMREGELTFNARLAKAFEDLNNVNT 354
                                           ***********************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (355 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: 20.06
//
[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 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