Alignments for a candidate for fba in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Acidovorax sp. GW101-3H11

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate Ac3H11_658 Fructose-bisphosphate aldolase class II (EC 4.1.2.13)

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_658
          Length = 349

 Score =  488 bits (1256), Expect = e-142
 Identities = 243/349 (69%), Positives = 287/349 (82%)

Query: 6   MRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEPFLRHL 65
           MR+LLDHAA +SYG+PAFNVNN+EQV+A+M AA    +PVILQ SAGARKYAGEPF++HL
Sbjct: 1   MRELLDHAAANSYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGEPFIKHL 60

Query: 66  IAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDYNVSVT 125
           I AAVEA+P IP+VMHQDHG SP VC GAI  GF SVMMDGSL EDGKTP+ ++YNV VT
Sbjct: 61  IQAAVEAFPHIPLVMHQDHGTSPKVCAGAIDLGFGSVMMDGSLMEDGKTPSSFEYNVEVT 120

Query: 126 AKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQFVKAT 185
            KVV++AH VGV+VEGELGCLG+LETG+   EDG GA+  LDHS++LTDP+EAA FVKAT
Sbjct: 121 RKVVDMAHKVGVTVEGELGCLGNLETGEAGEEDGIGADVKLDHSQMLTDPEEAAVFVKAT 180

Query: 186 QCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQELLEEI 245
           Q DALAIAIGTSHGAYKF+RKPTGDILAI R+K IH+RIP THLVMHGSSSVP ELL  I
Sbjct: 181 QLDALAIAIGTSHGAYKFSRKPTGDILAISRVKEIHKRIPNTHLVMHGSSSVPAELLAII 240

Query: 246 RTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFDPRKFM 305
             YGG +KETYGVPVEEIQE I++GVRK+NIDTDIRLAMT A+R+  A+N  +FD R+++
Sbjct: 241 NQYGGKMKETYGVPVEEIQEAIKHGVRKINIDTDIRLAMTGAVRKFLAENPDKFDAREWL 300

Query: 306 AAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVVH 354
             A E AK+VC AR+  FG  G+  KI+   L  +A +YASG LAQVV+
Sbjct: 301 KPAREAAKQVCKARYLEFGCEGQGAKIKGHSLQVVAAQYASGALAQVVN 349


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: 448
Number of extensions: 16
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: 349
Length adjustment: 29
Effective length of query: 325
Effective length of database: 320
Effective search space:   104000
Effective search space used:   104000
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 Ac3H11_658 (Fructose-bisphosphate aldolase class II (EC 4.1.2.13))
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.30523.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     3e-179  581.5   1.3   3.3e-179  581.3   1.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658  Fructose-bisphosphate aldolase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658  Fructose-bisphosphate aldolase class II (EC 4.1.2.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.3   1.3  3.3e-179  3.3e-179       4     347 .]       1     344 [.       1     344 [. 1.00

  Alignments for each domain:
  == domain 1  score: 581.3 bits;  conditional E-value: 3.3e-179
                                       TIGR01521   4 lrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvla 66 
                                                     +r lldhaa ++yg+pafnvnnleq+ a+m aad+  +pvilqas+gar+yage+++++l++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658   1 MRELLDHAAANSYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGEPFIKHLIQA 63 
                                                     8************************************************************** PP

                                       TIGR01521  67 aveeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvkl 129
                                                     ave +p+ip+v+hqdhg+sp++c  ai lgf svmmdgsl ed+ktp++++ynv+vt +vv +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658  64 AVEAFPHIPLVMHQDHGTSPKVCAGAIDLGFGSVMMDGSLMEDGKTPSSFEYNVEVTRKVVDM 126
                                                     *************************************************************** PP

                                       TIGR01521 130 ahavgasvegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavai 192
                                                     ah vg++vegelgclg letg++++edg g++ +ld+sq+ltdpeeaa fvk t++dala+ai
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658 127 AHKVGVTVEGELGCLGNLETGEAGEEDGIGADVKLDHSQMLTDPEEAAVFVKATQLDALAIAI 189
                                                     *************************************************************** PP

                                       TIGR01521 193 gtshgaykftrkptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketyg 255
                                                     gtshgaykf+rkptg++lai+r++eih+r+p+thlvmhgsssvp e l++in+ygg++ketyg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658 190 GTSHGAYKFSRKPTGDILAISRVKEIHKRIPNTHLVMHGSSSVPAELLAIINQYGGKMKETYG 252
                                                     *************************************************************** PP

                                       TIGR01521 256 vpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckary 318
                                                     vpveei++ ik+gvrk+nidtd rla+t+a+r+++a++p++fd r++lk+a ea k+vckary
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658 253 VPVEEIQEAIKHGVRKINIDTDIRLAMTGAVRKFLAENPDKFDAREWLKPAREAAKQVCKARY 315
                                                     *************************************************************** PP

                                       TIGR01521 319 eafgtagnaskikvvsleemarryakgel 347
                                                      +fg  g+ +kik  sl+ +a++ya+g l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_658 316 LEFGCEGQGAKIKGHSLQVVAAQYASGAL 344
                                                     **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (349 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.43
//
[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