GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Rhizobium johnstonii 3841

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011648981.1 RL_RS33900 class II fructose-bisphosphate aldolase

Query= BRENDA::A0Q7I9
         (354 letters)



>NCBI__GCF_000009265.1:WP_011648981.1
          Length = 354

 Score =  461 bits (1186), Expect = e-134
 Identities = 226/351 (64%), Positives = 274/351 (78%)

Query: 1   MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60
           MA ++LRQLLDHAAE GYG+PAFN+NN+EQ  A+MEAAD  ++PVI+Q S GAR YA   
Sbjct: 1   MARITLRQLLDHAAEEGYGVPAFNINNMEQALAIMEAADACHAPVIMQASRGARAYAHDI 60

Query: 61  FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120
            ++H++ A +E YPHIPVC+H DHG  PS C  +IQ GF+SVMMDGSLK+D KTPAD+ Y
Sbjct: 61  MLKHMMDAVVEIYPHIPVCVHLDHGNDPSNCMTAIQAGFTSVMMDGSLKADAKTPADWAY 120

Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180
           NV VTK V+DMAH  G+SVEGELG LGSLETG    EDG GAEG LS DQLLTDP+EA  
Sbjct: 121 NVGVTKMVTDMAHFGGISVEGELGVLGSLETGMGEAEDGHGAEGKLSHDQLLTDPDEAVK 180

Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240
           FVR TKVDALAIA+GTSHGAYKFT+ P G VL++  ++EIH ++P+THLVMHGSSSVP +
Sbjct: 181 FVRETKVDALAIAMGTSHGAYKFTRKPDGSVLAMNVIEEIHRKLPNTHLVMHGSSSVPIE 240

Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300
             E+IN YGG M  T+GVPVEEI   IK GVRK+NIDTD RMA TG IRR L E+P+EFD
Sbjct: 241 LQEIINKYGGQMKPTWGVPVEEIQRGIKNGVRKVNIDTDGRMAMTGQIRRVLQEDPSEFD 300

Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELDP 351
           PRKY   A  A++++C  R+E FG+AGMA +I P+ +  M +RY+SG LDP
Sbjct: 301 PRKYLKPAMTALTKLCKERFEQFGTAGMAGRITPLPVSEMAKRYKSGSLDP 351


Lambda     K      H
   0.316    0.132    0.380 

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: 483
Number of extensions: 11
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: 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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_011648981.1 RL_RS33900 (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.aa/TIGR01521.hmm
# target sequence database:        /tmp/gapView.4174820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-187  608.7   0.4   1.7e-187  608.5   0.4    1.0  1  NCBI__GCF_000009265.1:WP_011648981.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_011648981.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.5   0.4  1.7e-187  1.7e-187       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 608.5 bits;  conditional E-value: 1.7e-187
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           +i+lrqlldhaae+gygvpafn+nn+eq laimeaad++ +pvi+qasrgar ya + +l++++ a+ve yp+
  NCBI__GCF_000009265.1:WP_011648981.1   3 RITLRQLLDHAAEEGYGVPAFNINNMEQALAIMEAADACHAPVIMQASRGARAYAHDIMLKHMMDAVVEIYPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipv++h dhgn+p+ c++aiq gftsvmmdgslk+daktpad+ ynv vt+ v+ +ah  g+svegelg lgs
  NCBI__GCF_000009265.1:WP_011648981.1  76 IPVCVHLDHGNDPSNCMTAIQAGFTSVMMDGSLKADAKTPADWAYNVGVTKMVTDMAHFGGISVEGELGVLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg+geaedghg+eg+l + qlltdp+ea++fv++tkvdala+a+gtshgaykftrkp g vla+++ieeih
  NCBI__GCF_000009265.1:WP_011648981.1 149 LETGMGEAEDGHGAEGKLSHDQLLTDPDEAVKFVRETKVDALAIAMGTSHGAYKFTRKPDGSVLAMNVIEEIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           ++lp+thlvmhgsssvp e +++in+ygg++k t+gvpveei++gik gvrkvnidtd r+a+t+ +rrv+++
  NCBI__GCF_000009265.1:WP_011648981.1 222 RKLPNTHLVMHGSSSVPIELQEIINKYGGQMKPTWGVPVEEIQRGIKNGVRKVNIDTDGRMAMTGQIRRVLQE 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           dpsefdprk+lk+a+ a+ ++ck+r+e+fgtag a +i ++++ ema+ry +g+l
  NCBI__GCF_000009265.1:WP_011648981.1 295 DPSEFDPRKYLKPAMTALTKLCKERFEQFGTAGMAGRITPLPVSEMAKRYKSGSL 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: 22.64
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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