Alignments for a candidate for fbp in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Sinorhizobium medicae WSM419

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate YP_001313413.1 Smed_4683 fructose-1,6-bisphosphate aldolase

Query= BRENDA::Q55664
         (359 letters)



>NCBI__GCF_000017145.1:YP_001313413.1
          Length = 347

 Score =  474 bits (1220), Expect = e-138
 Identities = 231/345 (66%), Positives = 281/345 (81%)

Query: 1   MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60
           MAL+ +R LLDHAAEN Y +PAFNVNN+E I ++M+AAD TDSPVILQASRGAR+YAG+ 
Sbjct: 1   MALITLRQLLDHAAENNYALPAFNVNNLEYIQAVMRAADATDSPVILQASRGARAYAGDA 60

Query: 61  FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120
           FLRHL+LGAVE YPHIP+ +H DHG+ P+TC SAI NGFTSVMMDGSLE D KT AS+EY
Sbjct: 61  FLRHLILGAVEEYPHIPVCLHLDHGDQPSTCISAIINGFTSVMMDGSLEKDGKTVASYEY 120

Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180
           NV VTAEVVK+AH+ G SVEGELGCLG+LETG G+ EDGHGFEGKL   +LLTDPE+A++
Sbjct: 121 NVAVTAEVVKIAHAAGVSVEGELGCLGNLETGAGDKEDGHGFEGKLSREELLTDPEQALD 180

Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240
           FV+KT VDALAVAIGTSHGAYKFTR+P GE+L+I  I +I++ LPNTHLVMHGSSSVP  
Sbjct: 181 FVSKTGVDALAVAIGTSHGAYKFTREPDGEILSIETIAKINKRLPNTHLVMHGSSSVPAV 240

Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300
             ++ N +GG + +T+GVPV EIQK I  GVRKVNIDTD RLA T   R+   + P NFD
Sbjct: 241 LQELFNAYGGKMKKTWGVPVSEIQKAIPLGVRKVNIDTDLRLAFTGEIRKNHIEHPDNFD 300

Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYA 345
           PR++LKP+I +M +VC +R++ F +AG ASKI+ L L + A +YA
Sbjct: 301 PRNYLKPAIAHMAEVCKERFEAFRSAGQASKIRVLRLPEMAKRYA 345


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: 461
Number of extensions: 14
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: 347
Length adjustment: 29
Effective length of query: 330
Effective length of database: 318
Effective search space:   104940
Effective search space used:   104940
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 YP_001313413.1 Smed_4683 (fructose-1,6-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.15906.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-179  582.6   0.1   1.5e-179  582.4   0.1    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001313413.1  Smed_4683 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001313413.1  Smed_4683 fructose-1,6-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.4   0.1  1.5e-179  1.5e-179       1     344 [.       3     346 ..       3     347 .] 1.00

  Alignments for each domain:
  == domain 1  score: 582.4 bits;  conditional E-value: 1.5e-179
                                 TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 
                                               li+lrqlldhaae++y +pafnvnnle i a+m+aad+tdspvilqasrgar yag+++lr+l+l+ave
  lcl|NCBI__GCF_000017145.1:YP_001313413.1   3 LITLRQLLDHAAENNYALPAFNVNNLEYIQAVMRAADATDSPVILQASRGARAYAGDAFLRHLILGAVE 71 
                                               69******************************************************************* PP

                                 TIGR01521  70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138
                                               eyp+ipv+lh dhg++p+tc sai +gftsvmmdgsl++d+kt a+y+ynv vtaevvk+aha g+sve
  lcl|NCBI__GCF_000017145.1:YP_001313413.1  72 EYPHIPVCLHLDHGDQPSTCISAIINGFTSVMMDGSLEKDGKTVASYEYNVAVTAEVVKIAHAAGVSVE 140
                                               ********************************************************************* PP

                                 TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207
                                               gelgclg letg g++edghgfeg+l r +lltdpe+a +fv+kt+vdalavaigtshgaykftr+p g
  lcl|NCBI__GCF_000017145.1:YP_001313413.1 141 GELGCLGNLETGAGDKEDGHGFEGKLSREELLTDPEQALDFVSKTGVDALAVAIGTSHGAYKFTREPDG 209
                                               ********************************************************************* PP

                                 TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276
                                               e+l+i+ i +i +rlp+thlvmhgsssvp   ++++n+ygg++k+t+gvpv ei+k i  gvrkvnidt
  lcl|NCBI__GCF_000017145.1:YP_001313413.1 210 EILSIETIAKINKRLPNTHLVMHGSSSVPAVLQELFNAYGGKMKKTWGVPVSEIQKAIPLGVRKVNIDT 278
                                               ********************************************************************* PP

                                 TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryak 344
                                               dlrla t+ +r+   ++p++fdpr++lk+a+  m +vck+r+eaf +ag+aski+v+ l+ema+rya 
  lcl|NCBI__GCF_000017145.1:YP_001313413.1 279 DLRLAFTGEIRKNHIEHPDNFDPRNYLKPAIAHMAEVCKERFEAFRSAGQASKIRVLRLPEMAKRYAA 346
                                               ******************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (347 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.69
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis