Alignments for a candidate for fbp in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Teredinibacter turnerae T7901

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_015817193.1 TERTU_RS04210 class II fructose-bisphosphate aldolase

Query= BRENDA::A0KGD4
         (359 letters)



>NCBI__GCF_000023025.1:WP_015817193.1
          Length = 358

 Score =  615 bits (1585), Expect = 0.0
 Identities = 295/356 (82%), Positives = 324/356 (91%)

Query: 4   KIFDFVKPGVITGDDVQKVFAIAKENGFALPAVNCVGTDSVNAVLEAAAKVKAPVIVQFS 63
           K+ + VKPGV TGDDVQK+F IAK N FALPAVNCVGTDSVNAVLEAAAKVK+PV++QFS
Sbjct: 3   KVLEAVKPGVATGDDVQKIFEIAKANNFALPAVNCVGTDSVNAVLEAAAKVKSPVVIQFS 62

Query: 64  NGGAVFTAGKGLKLEGQQAAIIGAISGAKHVHAVAEAYGVPVILHTDHAAKKLLPWIDGL 123
           NGGA F AGKG+K EGQQA I+GAISGAKHVH VAEAYGVPVILHTDHAAKKLLPWIDGL
Sbjct: 63  NGGAAFFAGKGIKAEGQQAQILGAISGAKHVHQVAEAYGVPVILHTDHAAKKLLPWIDGL 122

Query: 124 LDAGEKHFAETGKPLFSSHMLDLSEESLEENIDICCEYLTRMAKMNMTLELELGCTGGEE 183
           LDAGEKHF ETGKPLFSSHMLDLSEESLEENI+IC +YL RM+KM MTLE+ELGCTGGEE
Sbjct: 123 LDAGEKHFEETGKPLFSSHMLDLSEESLEENIEICAKYLERMSKMGMTLEIELGCTGGEE 182

Query: 184 DGVDNSHMDQSALYTQPEDVAYAYERLSKISPRFTIAASFGNVHGVYKPGNVKLTPSILD 243
           DGVDNS MD S LYTQPEDVA+AYE+LS ISPRFTIAA+FGNVHGVYKPGNV+LTP ILD
Sbjct: 183 DGVDNSGMDSSELYTQPEDVAFAYEKLSAISPRFTIAAAFGNVHGVYKPGNVQLTPKILD 242

Query: 244 ASQKYVSEKFGIPAKSLDFVFHGGSGSTLEEIRESISYGVVKMNIDTDTQWATWEGILGF 303
            SQKY SEKFG+ A SL+FVFHGGSGST EEI+E+ISYGV+KMNIDTDTQWATWEG++ +
Sbjct: 243 NSQKYCSEKFGLGANSLNFVFHGGSGSTQEEIKEAISYGVIKMNIDTDTQWATWEGVMNY 302

Query: 304 YKKNEAYLQGQLGNPEGADKPNKKFYDPRVWLRAGQTTMIARLEKAFSDLNAIDVL 359
           YK+NE YLQGQ+GNPEG DKPNKK+YDPRVWLR GQ  MIARLE+AF DLNA+DVL
Sbjct: 303 YKENEGYLQGQIGNPEGEDKPNKKYYDPRVWLRKGQDAMIARLEQAFGDLNAVDVL 358


Lambda     K      H
   0.316    0.134    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: 478
Number of extensions: 6
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: 359
Length of database: 358
Length adjustment: 29
Effective length of query: 330
Effective length of database: 329
Effective search space:   108570
Effective search space used:   108570
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_015817193.1 TERTU_RS04210 (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.aa/TIGR01520.hmm
# target sequence database:        /tmp/gapView.2688182.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-186  606.1   0.6   1.2e-186  605.9   0.6    1.0  1  NCBI__GCF_000023025.1:WP_015817193.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023025.1:WP_015817193.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.9   0.6  1.2e-186  1.2e-186       1     356 [.       4     357 ..       4     358 .] 0.99

  Alignments for each domain:
  == domain 1  score: 605.9 bits;  conditional E-value: 1.2e-186
                             TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkd 73 
                                           vl+ +k+gv++g+dv+k+fe+ak ++fa+Pa+n+v++++vna+leaa+++ksp+++qfsnggaaf+aGkG+k 
  NCBI__GCF_000023025.1:WP_015817193.1   4 VLEAVKPGVATGDDVQKIFEIAKANNFALPAVNCVGTDSVNAVLEAAAKVKSPVVIQFSNGGAAFFAGKGIKA 76 
                                           57899******************************************************************** PP

                             TIGR01520  74 eaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlsee 146
                                           e ++a +i Gai++a++v+++ae+ygvpv+lhtdh akkllp++dgll+a+ek+f+++gkPlfsshmldlsee
  NCBI__GCF_000023025.1:WP_015817193.1  77 EGQQA-QILGAISGAKHVHQVAEAYGVPVILHTDHAAKKLLPWIDGLLDAGEKHFEETGKPLFSSHMLDLSEE 148
                                           ****9.9****************************************************************** PP

                             TIGR01520 147 pieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaa 219
                                           ++eeniei+ kyl+rm+k+ ++leie+G+tGGeedGvdn+ +d++elyt+Pedv  +ye+ls+isp+f+iaaa
  NCBI__GCF_000023025.1:WP_015817193.1 149 SLEENIEICAKYLERMSKMGMTLEIELGCTGGEEDGVDNSGMDSSELYTQPEDVAFAYEKLSAISPRFTIAAA 221
                                           ************************************************************************* PP

                             TIGR01520 220 fGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqy 292
                                           fGnvhGvykpGnv+l+P+il ++q+y +ek gl  a++l+fvfhGGsGst+eeikea+syGv+k+n+dtdtq+
  NCBI__GCF_000023025.1:WP_015817193.1 222 FGNVHGVYKPGNVQLTPKILDNSQKYCSEKFGLG-ANSLNFVFHGGSGSTQEEIKEAISYGVIKMNIDTDTQW 293
                                           *********************************9.99************************************ PP

                             TIGR01520 293 aalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                           a++eg+++y+++ne ylq+q+Gnp+ge+kpnkk+ydPrvwlr+++ +m+ar+e+a+ +lna+++
  NCBI__GCF_000023025.1:WP_015817193.1 294 ATWEGVMNYYKENEGYLQGQIGNPEGEDKPNKKYYDPRVWLRKGQDAMIARLEQAFGDLNAVDV 357
                                           ************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (358 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: 15.25
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis