Alignments for a candidate for fba in Megamonas funiformis YIT 11815

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Megamonas funiformis YIT 11815

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_008538557.1 HMPREF9454_RS06040 class II fructose-1,6-bisphosphate aldolase

Query= BRENDA::O97447
         (323 letters)



>NCBI__GCF_000245775.1:WP_008538557.1
          Length = 321

 Score =  291 bits (745), Expect = 1e-83
 Identities = 157/313 (50%), Positives = 206/313 (65%), Gaps = 15/313 (4%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           MPL T ++M  +A +  Y +GAFNVNNME +QGI +A  +L +P+ILQCS GA KY+   
Sbjct: 1   MPLVTTKEMFKKAYEGHYAIGAFNVNNMEIVQGITEAAKELNAPLILQCSAGARKYAKHQ 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           YL  L +AA+E    +PI +HLDHG   E+ K  ID GF+SVM D SH+ F EN+  TKE
Sbjct: 61  YLVHLVQAAIED-TGLPIALHLDHGADFETCKSCIDGGFTSVMFDGSHYSFKENIEKTKE 119

Query: 121 VVAYAHARSVSVEAELGTLGGIEEDVQ---NTVQLTEPQDAKKFVELTGVDALAVAIGTS 177
           VV YAHA  V VEAELG L GIE+DV+   +    T+P + ++FV+ TGVD+LA+AIGTS
Sbjct: 120 VVEYAHAHGVVVEAELGQLAGIEDDVKVAAHEAHYTDPNEVEEFVKETGVDSLAIAIGTS 179

Query: 178 HGAYKFKSESDIR----------LAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKY 226
           HGAYKF  +   R          L  D ++ ++  L   P+V+HG+SSVP+D   +IN+ 
Sbjct: 180 HGAYKFTPDQCTRNEQGILVPPPLRFDILEEVAKRLPNFPIVLHGASSVPQDFVKIINEN 239

Query: 227 GGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPG 286
           GG MPDAVGVP + +  A    VCKIN+DSD R+AMT  IRK F +HP+ FDPR Y+  G
Sbjct: 240 GGHMPDAVGVPEDQLRKAASMAVCKINIDSDLRLAMTAGIRKHFNDHPDHFDPRQYVADG 299

Query: 287 RDAITEMLIPKIK 299
           R  I  ++  KIK
Sbjct: 300 RTNIKAIVSHKIK 312


Lambda     K      H
   0.318    0.135    0.389 

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: 347
Number of extensions: 12
Number of successful extensions: 4
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: 323
Length of database: 321
Length adjustment: 28
Effective length of query: 295
Effective length of database: 293
Effective search space:    86435
Effective search space used:    86435
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_008538557.1 HMPREF9454_RS06040 (class II fructose-1,6-bisphosphate aldolase)
to HMM TIGR01859 (fba: fructose-1,6-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/TIGR01859.hmm
# target sequence database:        /tmp/gapView.1637436.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01859  [M=282]
Accession:   TIGR01859
Description: fruc_bis_ald_: fructose-1,6-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-114  366.0   0.5     1e-113  365.7   0.5    1.1  1  NCBI__GCF_000245775.1:WP_008538557.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000245775.1:WP_008538557.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.7   0.5    1e-113    1e-113       1     282 []       3     321 .]       3     321 .] 0.98

  Alignments for each domain:
  == domain 1  score: 365.7 bits;  conditional E-value: 1e-113
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv++ke+++ka++++Ya+gafn+nn+e++q i eaa+e ++P+i+q s ga+kY+   + +v+lv+a+ie++ 
  NCBI__GCF_000245775.1:WP_008538557.1   3 LVTTKEMFKKAYEGHYAIGAFNVNNMEIVQGITEAAKELNAPLILQCSAGARKYAK-HQYLVHLVQAAIEDTG 74 
                                           79*****************************************************9.99************99 PP

                             TIGR01859  74 ivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGiedd.. 144
                                            +P+alhLDhG ++e+c ++i+ Gf+svm+D+sh+++ en+++tk+vve+aha+gv veaelG+l+Giedd  
  NCBI__GCF_000245775.1:WP_008538557.1  75 -LPIALHLDHGADFETCKSCIDGGFTSVMFDGSHYSFKENIEKTKEVVEYAHAHGVVVEAELGQLAGIEDDvk 146
                                           .**********************************************************************77 PP

                             TIGR01859 145 vvekeaeladideakklvketgvDaLaiaiGtshGkykge..............pkldferlkeikklln.lP 202
                                           v ++ea+++d++e++++vketgvD+LaiaiGtshG yk                p l+f+ l+e+ k+l+ +P
  NCBI__GCF_000245775.1:WP_008538557.1 147 VAAHEAHYTDPNEVEEFVKETGVDSLAIAIGTSHGAYKFTpdqctrneqgilvpPPLRFDILEEVAKRLPnFP 219
                                           8899*******************************666655699**********************99988** PP

                             TIGR01859 203 lvlhGas.....................Gipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydp 254
                                           +vlhGas                     G+pe+ql+ka++++++k+nid+dlrla+ta irk+++++ d++dp
  NCBI__GCF_000245775.1:WP_008538557.1 220 IVLHGASsvpqdfvkiinengghmpdavGVPEDQLRKAASMAVCKINIDSDLRLAMTAGIRKHFNDHPDHFDP 292
                                           ************************************************************************* PP

                             TIGR01859 255 Rkilaparealkevvkekik.vlgsagka 282
                                           R+++a++r ++k++v +kik vlg  gka
  NCBI__GCF_000245775.1:WP_008538557.1 293 RQYVADGRTNIKAIVSHKIKeVLGCDGKA 321
                                           *******************9889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (321 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.72
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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