GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Gracilibacillus halophilus YIM-C55.5

Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_003473390.1 J416_RS13030 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::P13243
         (285 letters)



>NCBI__GCF_000359605.1:WP_003473390.1
          Length = 285

 Score =  456 bits (1172), Expect = e-133
 Identities = 227/285 (79%), Positives = 250/285 (87%), Gaps = 1/285 (0%)

Query: 1   MPLVSMTEMLNTAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGF 60
           MPLVSM EML  A +  Y VGQFNLNNLE+ QAILQAAEEE+SPVILGVSEGAG+YMGGF
Sbjct: 1   MPLVSMKEMLEDANKNRYGVGQFNLNNLEYAQAILQAAEEEQSPVILGVSEGAGKYMGGF 60

Query: 61  KTVVAMVKALMEEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATT 120
           K VV+MVKALMEEY  TVPVAIHLDHGSSFE+CAKAIHAGFTSVMIDASH PFEENVA T
Sbjct: 61  KVVVSMVKALMEEYGTTVPVAIHLDHGSSFEACAKAIHAGFTSVMIDASHDPFEENVALT 120

Query: 121 AKVVELAHFHGVSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSV 180
           +KVVELAHFHGVSVEAELGTVGG ED V   G+IYAD  EC+ELVERTG+DCLAPALGSV
Sbjct: 121 SKVVELAHFHGVSVEAELGTVGGTEDGVTG-GIIYADANECKELVERTGVDCLAPALGSV 179

Query: 181 HGPYKGEPNLGFKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQISS 240
           HGPY+GEPNLGFKEMEEI    G+PLVLHGGTGIP+ DIKK++S GT+KINVNTENQ++ 
Sbjct: 180 HGPYQGEPNLGFKEMEEINTVAGVPLVLHGGTGIPSEDIKKALSFGTSKINVNTENQMAQ 239

Query: 241 AKAVRETLAAKPDEYDPRKYLGPAREAIKETVIGKMREFGSSNQA 285
            +AVR+ L  KP+ YDPRKYLGP R+AIKE VIGKMREF SSN+A
Sbjct: 240 TEAVRKVLKEKPELYDPRKYLGPGRDAIKEIVIGKMREFSSSNKA 284


Lambda     K      H
   0.313    0.131    0.367 

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: 395
Number of extensions: 10
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: 285
Length of database: 285
Length adjustment: 26
Effective length of query: 259
Effective length of database: 259
Effective search space:    67081
Effective search space used:    67081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_003473390.1 J416_RS13030 (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.1255922.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-132  427.0   0.7   2.4e-132  426.8   0.7    1.0  1  NCBI__GCF_000359605.1:WP_003473390.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359605.1:WP_003473390.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.8   0.7  2.4e-132  2.4e-132       1     282 []       3     284 ..       3     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 426.8 bits;  conditional E-value: 2.4e-132
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv++ke+le+a+k++Y+vg+fn+nnle++qail+aaeee+sPvi+ vsega kY+gg+kvvv++vkal+e++ 
  NCBI__GCF_000359605.1:WP_003473390.1   3 LVSMKEMLEDANKNRYGVGQFNLNNLEYAQAILQAAEEEQSPVILGVSEGAGKYMGGFKVVVSMVKALMEEYG 75 
                                           79**********************************************************************9 PP

                             TIGR01859  74 i.vPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddv 145
                                           + vPva+hLDhGss+e+c+kai+aGf+svmiDash p+een+++t+kvve+ah +gvsveaelG++gG+ed+v
  NCBI__GCF_000359605.1:WP_003473390.1  76 TtVPVAIHLDHGSSFEACAKAIHAGFTSVMIDASHDPFEENVALTSKVVELAHFHGVSVEAELGTVGGTEDGV 148
                                           99*********************************************************************** PP

                             TIGR01859 146 vekeaeladideakklvketgvDaLaiaiGtshGkykgepkldferlkeikkllnlPlvlhGasGipeeqlkk 218
                                           ++    +ad +e+k+lv++tgvD+La+a+G++hG+y+gep+l f++++ei+ +  +PlvlhG++Gip+e++kk
  NCBI__GCF_000359605.1:WP_003473390.1 149 TG-GIIYADANECKELVERTGVDCLAPALGSVHGPYQGEPNLGFKEMEEINTVAGVPLVLHGGTGIPSEDIKK 220
                                           **.9********************************************************************* PP

                             TIGR01859 219 aiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekikvlgsagka 282
                                           a++ g++k+n++t++++a t+a+rkvl+ek + ydpRk+l+p+r+a+ke+v+ k++++ s++ka
  NCBI__GCF_000359605.1:WP_003473390.1 221 ALSFGTSKINVNTENQMAQTEAVRKVLKEKPELYDPRKYLGPGRDAIKEIVIGKMREFSSSNKA 284
                                           **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (285 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: 17.75
//
[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