GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Rhodobacter viridis JA737

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_110804069.1 C8J30_RS02175 fructose-bisphosphate aldolase class II

Query= BRENDA::Q55664
         (359 letters)



>NCBI__GCF_003217355.1:WP_110804069.1
          Length = 354

 Score =  481 bits (1238), Expect = e-140
 Identities = 236/349 (67%), Positives = 284/349 (81%)

Query: 1   MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60
           MAL+ +R LLDHAAE  YG+PAFN+NNMEQ ++IM+AA   D+PVI+QASRGARSYA + 
Sbjct: 1   MALITLRQLLDHAAEYSYGVPAFNINNMEQGLAIMEAAKAVDAPVIIQASRGARSYANDI 60

Query: 61  FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120
            L  ++      YP IP+ MHQDHGN+ ATC +AIR+GFTSVMMDGSLE DAKTPAS+EY
Sbjct: 61  MLAKMIEALAAIYPDIPLCMHQDHGNNEATCMTAIRHGFTSVMMDGSLEGDAKTPASYEY 120

Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180
           NV++T  V ++AH VGASVEGELG LGSLETGQGEAEDGHG EG LDHSQLLTDP++AV+
Sbjct: 121 NVDITERVSRMAHWVGASVEGELGVLGSLETGQGEAEDGHGAEGVLDHSQLLTDPDQAVD 180

Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240
           FV KTQVDALA+A GTSHGAYKF+RKP GE+LA+S IE IH+ LPNTHLVMHGSSSVPQ+
Sbjct: 181 FVKKTQVDALAIACGTSHGAYKFSRKPDGEILAMSVIEAIHKKLPNTHLVMHGSSSVPQD 240

Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300
             D+INEFGGA+P+T+GVPVEEI +GIK GVRKVNIDTD R+A+T  FR  A ++   FD
Sbjct: 241 LQDIINEFGGAMPQTFGVPVEEIVRGIKMGVRKVNIDTDCRMAMTGQFRRIAEQNKAEFD 300

Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYAKGEL 349
           PR FLKP++  M+ +C  R + F TAG+ASKIK + +DD A +YA G L
Sbjct: 301 PRKFLKPAMDAMRDLCRARLEAFGTAGHASKIKVIPMDDMAKRYASGSL 349


Lambda     K      H
   0.315    0.131    0.377 

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: 447
Number of extensions: 13
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: 354
Length adjustment: 29
Effective length of query: 330
Effective length of database: 325
Effective search space:   107250
Effective search space used:   107250
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_110804069.1 C8J30_RS02175 (fructose-bisphosphate aldolase class II)
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.1068811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-200  650.0   1.1   4.8e-200  649.8   1.1    1.0  1  NCBI__GCF_003217355.1:WP_110804069.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110804069.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  649.8   1.1  4.8e-200  4.8e-200       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 649.8 bits;  conditional E-value: 4.8e-200
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           li+lrqlldhaae +ygvpafn+nn+eq laimeaa++ d+pvi+qasrgarsya++ +l+k+++a+   ypd
  NCBI__GCF_003217355.1:WP_110804069.1   3 LITLRQLLDHAAEYSYGVPAFNINNMEQGLAIMEAAKAVDAPVIIQASRGARSYANDIMLAKMIEALAAIYPD 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ip+++hqdhgn+ atc++ai++gftsvmmdgsl+ daktpa+y+ynv++t++v+++ah vgasvegelg lgs
  NCBI__GCF_003217355.1:WP_110804069.1  76 IPLCMHQDHGNNEATCMTAIRHGFTSVMMDGSLEGDAKTPASYEYNVDITERVSRMAHWVGASVEGELGVLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg+geaedghg+eg+ld+sqlltdp++a++fvkkt+vdala+a gtshgaykf+rkp ge+la+++ie ih
  NCBI__GCF_003217355.1:WP_110804069.1 149 LETGQGEAEDGHGAEGVLDHSQLLTDPDQAVDFVKKTQVDALAIACGTSHGAYKFSRKPDGEILAMSVIEAIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           ++lp+thlvmhgsssvpq+ +d+ine+gg++++t+gvpveeiv+gik+gvrkvnidtd r+a+t+ +rr+a++
  NCBI__GCF_003217355.1:WP_110804069.1 222 KKLPNTHLVMHGSSSVPQDLQDIINEFGGAMPQTFGVPVEEIVRGIKMGVRKVNIDTDCRMAMTGQFRRIAEQ 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           ++ efdprkflk+a++am+d+c ar eafgtag askikv+++++ma+rya+g+l
  NCBI__GCF_003217355.1:WP_110804069.1 295 NKAEFDPRKFLKPAMDAMRDLCRARLEAFGTAGHASKIKVIPMDDMAKRYASGSL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.76
//
[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