Alignments for a candidate for fbp in Methylomicrobium alcaliphilum 20Z

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Methylomicrobium alcaliphilum 20Z

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_014150352.1 MEALZ_RS19370 class II fructose-bisphosphate aldolase

Query= BRENDA::A0KGD4
         (359 letters)



>NCBI__GCF_000968535.2:WP_014150352.1
          Length = 359

 Score =  580 bits (1496), Expect = e-170
 Identities = 280/359 (77%), Positives = 317/359 (88%)

Query: 1   MSKKIFDFVKPGVITGDDVQKVFAIAKENGFALPAVNCVGTDSVNAVLEAAAKVKAPVIV 60
           M++KI D VKPGV+TG+DVQKVFA  KE+ FALPAVN + TD++N+VLE+AAK K+PVI+
Sbjct: 1   MAQKILDIVKPGVVTGEDVQKVFAFCKEHKFALPAVNVISTDTINSVLESAAKAKSPVII 60

Query: 61  QFSNGGAVFTAGKGLKLEGQQAAIIGAISGAKHVHAVAEAYGVPVILHTDHAAKKLLPWI 120
           QFSNGGA F AGKG+ LEGQ  +I+GAISGA+HVH +AE YGVPVILHTDHAAKKLLPWI
Sbjct: 61  QFSNGGAAFFAGKGVNLEGQMPSILGAISGAQHVHLMAEHYGVPVILHTDHAAKKLLPWI 120

Query: 121 DGLLDAGEKHFAETGKPLFSSHMLDLSEESLEENIDICCEYLTRMAKMNMTLELELGCTG 180
           DGLLDAGEKHF +TGKPLFSSHMLDLSEESLEENI+IC +YL RM+KM+MTLE+ELG TG
Sbjct: 121 DGLLDAGEKHFEKTGKPLFSSHMLDLSEESLEENIEICGKYLERMSKMDMTLEIELGVTG 180

Query: 181 GEEDGVDNSHMDQSALYTQPEDVAYAYERLSKISPRFTIAASFGNVHGVYKPGNVKLTPS 240
           GEEDGVDN+ MD S LYTQPEDVAYAYE LSKIS RFTIAASFGNVHGVYKPGNVKLTP+
Sbjct: 181 GEEDGVDNTDMDHSLLYTQPEDVAYAYENLSKISHRFTIAASFGNVHGVYKPGNVKLTPT 240

Query: 241 ILDASQKYVSEKFGIPAKSLDFVFHGGSGSTLEEIRESISYGVVKMNIDTDTQWATWEGI 300
           IL  SQKYVSEKF +P  SL FVFHGGSGS+ EEI+ESISYGVVKMNIDTDTQWATW G+
Sbjct: 241 ILRDSQKYVSEKFSLPENSLTFVFHGGSGSSPEEIKESISYGVVKMNIDTDTQWATWAGV 300

Query: 301 LGFYKKNEAYLQGQLGNPEGADKPNKKFYDPRVWLRAGQTTMIARLEKAFSDLNAIDVL 359
           + FYKKNE YLQGQ+GNP+G DKPNKK+YDPRVW RAGQ  M+ RL++AF DLNA + L
Sbjct: 301 MEFYKKNEGYLQGQIGNPDGDDKPNKKYYDPRVWQRAGQVGMVTRLQQAFQDLNASNTL 359


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: 480
Number of extensions: 11
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: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
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_014150352.1 MEALZ_RS19370 (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.26608.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-182  591.7   0.2   2.6e-182  591.6   0.2    1.0  1  lcl|NCBI__GCF_000968535.2:WP_014150352.1  MEALZ_RS19370 class II fructose-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_014150352.1  MEALZ_RS19370 class II fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.6   0.2  2.6e-182  2.6e-182       1     356 [.       5     358 ..       5     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 591.6 bits;  conditional E-value: 2.6e-182
                                 TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGk 69 
                                               +ld++k+gv++gedv+k+f  +ke+kfa+Pa+nv+s++t+n++le+a++aksp+i+qfsnggaaf+aGk
  lcl|NCBI__GCF_000968535.2:WP_014150352.1   5 ILDIVKPGVVTGEDVQKVFAFCKEHKFALPAVNVISTDTINSVLESAAKAKSPVIIQFSNGGAAFFAGK 73 
                                               6799***************************************************************** PP

                                 TIGR01520  70 GvkdeaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfss 138
                                               Gv+ e +   si Gai++a++v+ +ae+ygvpv+lhtdh akkllp++dgll+a+ek+f+k+gkPlfss
  lcl|NCBI__GCF_000968535.2:WP_014150352.1  74 GVNLEGQMP-SILGAISGAQHVHLMAEHYGVPVILHTDHAAKKLLPWIDGLLDAGEKHFEKTGKPLFSS 141
                                               ****88877.*********************************************************** PP

                                 TIGR01520 139 hmldlseepieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeel 207
                                               hmldlsee++eeniei+ kyl+rm+k++++leie+G+tGGeedGvdn ++d++ lyt+Pedv ++ye+l
  lcl|NCBI__GCF_000968535.2:WP_014150352.1 142 HMLDLSEESLEENIEICGKYLERMSKMDMTLEIELGVTGGEEDGVDNTDMDHSLLYTQPEDVAYAYENL 210
                                               ********************************************************************* PP

                                 TIGR01520 208 skispkfsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikea 276
                                               skis +f+iaa+fGnvhGvykpGnvkl+P+il+d+q+yv+ek +l+ +++l+fvfhGGsGs+ eeike+
  lcl|NCBI__GCF_000968535.2:WP_014150352.1 211 SKISHRFTIAASFGNVHGVYKPGNVKLTPTILRDSQKYVSEKFSLP-ENSLTFVFHGGSGSSPEEIKES 278
                                               **********************************************.99******************** PP

                                 TIGR01520 277 lsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarve 345
                                               +syGvvk+n+dtdtq+a++ g++++++kne ylq+q+Gnp+g +kpnkk+ydPrvw r++++ m  r++
  lcl|NCBI__GCF_000968535.2:WP_014150352.1 279 ISYGVVKMNIDTDTQWATWAGVMEFYKKNEGYLQGQIGNPDGDDKPNKKYYDPRVWQRAGQVGMVTRLQ 347
                                               ********************************************************************* PP

                                 TIGR01520 346 kaleelnaink 356
                                               +a+++lna n+
  lcl|NCBI__GCF_000968535.2:WP_014150352.1 348 QAFQDLNASNT 358
                                               *******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (359 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: 00:00:00.01
# Mc/sec: 8.79
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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