GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Hydrogenovibrio kuenenii DSM 12350

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_024850292.1 N745_RS0101050 class II fructose-bisphosphate aldolase

Query= BRENDA::Q602L6
         (354 letters)



>NCBI__GCF_000526715.1:WP_024850292.1
          Length = 354

 Score =  514 bits (1324), Expect = e-150
 Identities = 244/350 (69%), Positives = 297/350 (84%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MA+I+LR+L+D+AAE+ +G+PAFNVNNMEQ++AIM AA A D+PVILQGSAGAR YAGEP
Sbjct: 1   MAMITLRELMDYAAENSFGMPAFNVNNMEQVRAIMRAADACDSPVILQGSAGARKYAGEP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
            LRH++ AA EMYPHIPV MHQDHG+   VC+R+IQSGF+SVMMDGSL  DMKTPASY Y
Sbjct: 61  MLRHMIEAATEMYPHIPVVMHQDHGSDVGVCLRAIQSGFTSVMMDGSLESDMKTPASYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           N   T +VV++AHA GVSVEGELGCLGSLETG+ G+EDGHG++ ELDHS+LLTDP+EAA 
Sbjct: 121 NAGITAEVVKIAHAGGVSVEGELGCLGSLETGKMGEEDGHGSDEELDHSMLLTDPEEAAQ 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV+ T VDALA+A+GTSHGAYKFT KP+  VL+ID++  IH+RIP  H+VMHGSSSVPEE
Sbjct: 181 FVKDTNVDALAVAVGTSHGAYKFTSKPSDDVLKIDQIAKIHKRIPDTHIVMHGSSSVPEE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN+YGGD+GQTYGVPVE IVEGI+HGVRKVNIDTDLR+AS GA+R+ + ++  NFD
Sbjct: 241 WLEIINNYGGDMGQTYGVPVEAIVEGIKHGVRKVNIDTDLRMASTGAIRKHLHDNPANFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLD 350
           PRK + AA+ AM  IC+AR+EAFG AG A+KIK + LE+M   YA G LD
Sbjct: 301 PRKFFNAAENAMLEICKARFEAFGCAGHASKIKSVGLEEMQARYASGSLD 350


Lambda     K      H
   0.320    0.134    0.391 

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: 470
Number of extensions: 19
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: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_024850292.1 N745_RS0101050 (class II fructose-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (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/TIGR01521.hmm
# target sequence database:        /tmp/gapView.3151893.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01521  [M=347]
Accession:   TIGR01521
Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-188  612.2   2.2   1.5e-188  612.0   2.2    1.0  1  NCBI__GCF_000526715.1:WP_024850292.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000526715.1:WP_024850292.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.0   2.2  1.5e-188  1.5e-188       2     347 .]       4     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 612.0 bits;  conditional E-value: 1.5e-188
                             TIGR01521   2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdi 74 
                                           i+lr l+d+aae+++g+pafnvnn+eq++aim+aad++dspvilq s+gar+yage++lr++++aa e+yp+i
  NCBI__GCF_000526715.1:WP_024850292.1   4 ITLRELMDYAAENSFGMPAFNVNNMEQVRAIMRAADACDSPVILQGSAGARKYAGEPMLRHMIEAATEMYPHI 76 
                                           99*********************************************************************** PP

                             TIGR01521  75 pvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsl 147
                                           pvv+hqdhg+++ +cl+aiq gftsvmmdgsl+ d ktpa+y+yn  +taevvk+aha g+svegelgclgsl
  NCBI__GCF_000526715.1:WP_024850292.1  77 PVVMHQDHGSDVGVCLRAIQSGFTSVMMDGSLESDMKTPASYEYNAGITAEVVKIAHAGGVSVEGELGCLGSL 149
                                           ************************************************************************* PP

                             TIGR01521 148 etgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeihe 220
                                           etgk ++edghg +  ld+s lltdpeeaa+fvk+t+vdalava+gtshgaykft kp+ +vl id+i +ih+
  NCBI__GCF_000526715.1:WP_024850292.1 150 ETGKMGEEDGHGSDEELDHSMLLTDPEEAAQFVKDTNVDALAVAVGTSHGAYKFTSKPSDDVLKIDQIAKIHK 222
                                           ************************************************************************* PP

                             TIGR01521 221 rlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakd 293
                                           r+pdth+vmhgsssvp+ewl++in+ygg++ +tygvpve iv+gik+gvrkvnidtdlr+a+t+a+r+ + ++
  NCBI__GCF_000526715.1:WP_024850292.1 223 RIPDTHIVMHGSSSVPEEWLEIINNYGGDMGQTYGVPVEAIVEGIKHGVRKVNIDTDLRMASTGAIRKHLHDN 295
                                           ************************************************************************* PP

                             TIGR01521 294 psefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           p +fdprkf++ a +am ++ckar+eafg ag askik+v leem +rya+g+l
  NCBI__GCF_000526715.1:WP_024850292.1 296 PANFDPRKFFNAAENAMLEICKARFEAFGCAGHASKIKSVGLEEMQARYASGSL 349
                                           ****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.19
//
[ok]

This GapMind analysis is from Apr 09 2024. 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