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.3097348.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: 18.20
//
[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:

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:

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:

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:

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