Alignments for a candidate for fba in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Herbaspirillum seropedicae SmR1

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate HSERO_RS03355 HSERO_RS03355 fructose-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__HerbieS:HSERO_RS03355
          Length = 354

 Score =  521 bits (1343), Expect = e-153
 Identities = 262/353 (74%), Positives = 300/353 (84%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           M LVSMRQLLDHAA++ YGLPAFNVNN+EQV AIM+AA    +PVI+Q SAGARKYAGE 
Sbjct: 1   MPLVSMRQLLDHAAENGYGLPAFNVNNLEQVTAIMEAANEVGAPVIMQASAGARKYAGEA 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           FLRHLI+AAVEAYP IPVVMHQDHG SPAVCM AIKSGFSSVMMDGSL+ DGKT A Y+Y
Sbjct: 61  FLRHLISAAVEAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLEADGKTVASYEY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV V+ KVVE +HA+GV+VE ELG LGSLET KG+ EDGHGA+  +   +LLTD ++AA 
Sbjct: 121 NVEVSRKVVEFSHAIGVTVEAELGVLGSLETMKGDKEDGHGADGTMTREQLLTDVNQAAD 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FVKATQCDALAIAIGTSHGAYKF+RKPTGDILAIDRIK IH RIP THLVMHGSSSVPQE
Sbjct: 181 FVKATQCDALAIAIGTSHGAYKFSRKPTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           LL EIR +GGD+KETYGVPVEEIQEGI++GVRK+NIDTDIRLAMT AIRR   +N S+FD
Sbjct: 241 LLAEIREFGGDMKETYGVPVEEIQEGIKHGVRKINIDTDIRLAMTGAIRRYLFENPSKFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353
           PR ++  A E AK VC ARF +FG  G+A KI+ I L+++A++Y SGELAQ+V
Sbjct: 301 PRDYLKPAREAAKLVCKARFLSFGCEGQAGKIKPISLEKIAEKYKSGELAQIV 353


Lambda     K      H
   0.316    0.132    0.369 

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: 463
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: 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 HSERO_RS03355 HSERO_RS03355 (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.32555.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.1e-181  588.6   0.9   2.3e-181  588.4   0.9    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS03355  HSERO_RS03355 fructose-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS03355  HSERO_RS03355 fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.4   0.9  2.3e-181  2.3e-181       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 588.4 bits;  conditional E-value: 2.3e-181
                                  TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaav 68 
                                                l+s+rqlldhaae+gyg+pafnvnnleq+ aimeaa++  +pvi+qas+gar+yage++lr+l+ aav
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355   3 LVSMRQLLDHAAENGYGLPAFNVNNLEQVTAIMEAANEVGAPVIMQASAGARKYAGEAFLRHLISAAV 70 
                                                69****************************************************************** PP

                                  TIGR01521  69 eeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgas 136
                                                e yp+ipvv+hqdhg+spa+c++ai+ gf+svmmdgsl++d+kt a+y+ynv+v+ +vv+++ha+g++
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355  71 EAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLEADGKTVASYEYNVEVSRKVVEFSHAIGVT 138
                                                ******************************************************************** PP

                                  TIGR01521 137 vegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrk 204
                                                ve elg lgslet kg++edghg++g++ r qlltd ++aa+fvk t+ dala+aigtshgaykf+rk
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 139 VEAELGVLGSLETMKGDKEDGHGADGTMTREQLLTDVNQAADFVKATQCDALAIAIGTSHGAYKFSRK 206
                                                ******************************************************************** PP

                                  TIGR01521 205 ptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkv 272
                                                ptg++laidri+eih+r+p+thlvmhgsssvpqe l+ i e+gg++ketygvpveei++gik+gvrk+
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 207 PTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQELLAEIREFGGDMKETYGVPVEEIQEGIKHGVRKI 274
                                                ******************************************************************** PP

                                  TIGR01521 273 nidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemar 340
                                                nidtd rla+t+a+rr + ++ps+fdpr +lk+a ea k vckar+ +fg  g+a kik++sle++a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 275 NIDTDIRLAMTGAIRRYLFENPSKFDPRDYLKPAREAAKLVCKARFLSFGCEGQAGKIKPISLEKIAE 342
                                                ******************************************************************** PP

                                  TIGR01521 341 ryakgel 347
                                                +y +gel
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 343 KYKSGEL 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.16
//
[ok]

This GapMind analysis is from Sep 17 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:

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

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 catabolism of small carbon sources