Alignments for a candidate for fba in Geobacter lovleyi SZ

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Geobacter lovleyi SZ

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_012469022.1 GLOV_RS04670 fructose-1,6-bisphosphate aldolase, class II

Query= BRENDA::O97447
         (323 letters)



>NCBI__GCF_000020385.1:WP_012469022.1
          Length = 325

 Score =  270 bits (691), Expect = 3e-77
 Identities = 145/313 (46%), Positives = 204/313 (65%), Gaps = 8/313 (2%)

Query: 3   LCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYL 62
           L   ++M  +A   KY + A+N NN+EQ+Q I+ A V+  SPVI+Q S+GA  Y++   L
Sbjct: 13  LVNTKEMFAKAMAGKYAIPAYNFNNLEQLQAIVVACVETNSPVIIQVSKGARSYANETML 72

Query: 63  KKLCEAALEKHPD----IPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRIT 118
           + +   A++   +    IPIC+HLDHGD+ E  K  +D GFSSVMID SH P+DENV + 
Sbjct: 73  RYMAMGAVQMARELGSTIPICLHLDHGDSFELCKSCVDSGFSSVMIDGSHLPYDENVALC 132

Query: 119 KEVVAYAHARSVSVEAELGTLGGIEEDVQ-NTVQLTEPQDAKKFVELTGVDALAVAIGTS 177
           K+VV YAH   VSVE ELG L GIE++V       T+P++ + FV+ TGVD+LA++IGTS
Sbjct: 133 KKVVEYAHQFDVSVEGELGVLAGIEDEVSAEHSTYTKPEEVEDFVKKTGVDSLAISIGTS 192

Query: 178 HGAYKFKSESDI-RLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVG 235
           HGAYKFK+   +  L  D +      L G P+V+HG+SSV ++  ++IN+ GGKM  AVG
Sbjct: 193 HGAYKFKAGQPVPPLRFDILAECEKRLPGFPIVLHGASSVVQEYVELINQNGGKMEGAVG 252

Query: 236 VPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLI 295
           VP E +  A    VCKIN+DSD R+A+T  +R+ F + P++FDPR YLG  R  + +++ 
Sbjct: 253 VPEEQLRQAAASAVCKINIDSDGRLAVTAKVREYFGKDPKEFDPRKYLGEARKELIKLIK 312

Query: 296 PKIK-AFGSAGHA 307
            K +   GSAG A
Sbjct: 313 HKNETVLGSAGKA 325


Lambda     K      H
   0.318    0.135    0.389 

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: 300
Number of extensions: 14
Number of successful extensions: 4
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: 323
Length of database: 325
Length adjustment: 28
Effective length of query: 295
Effective length of database: 297
Effective search space:    87615
Effective search space used:    87615
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_012469022.1 GLOV_RS04670 (fructose-1,6-bisphosphate aldolase, class II)
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (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/TIGR01859.hmm
# target sequence database:        /tmp/gapView.25236.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01859  [M=282]
Accession:   TIGR01859
Description: fruc_bis_ald_: fructose-1,6-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-116  375.1   0.2   1.8e-116  374.8   0.2    1.1  1  lcl|NCBI__GCF_000020385.1:WP_012469022.1  GLOV_RS04670 fructose-1,6-bispho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012469022.1  GLOV_RS04670 fructose-1,6-bisphosphate aldolase, class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.8   0.2  1.8e-116  1.8e-116       1     282 []      13     325 .]      13     325 .] 0.98

  Alignments for each domain:
  == domain 1  score: 374.8 bits;  conditional E-value: 1.8e-116
                                 TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg...gikvvvalvk 66 
                                               lv++ke+++ka ++kYa++a+n+nnle+lqai+ a+ e++sPvi+qvs+ga+ Y++   ++ +++++v+
  lcl|NCBI__GCF_000020385.1:WP_012469022.1  13 LVNTKEMFAKAMAGKYAIPAYNFNNLEQLQAIVVACVETNSPVIIQVSKGARSYANetmLRYMAMGAVQ 81 
                                               79******************************************************88778899999** PP

                                 TIGR01859  67 alieklsivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveael 135
                                                + e  s++P++lhLDhG+s+e c +++++GfssvmiD+shlp++en+++ kkvve+ah+  vsve el
  lcl|NCBI__GCF_000020385.1:WP_012469022.1  82 MARELGSTIPICLHLDHGDSFELCKSCVDSGFSSVMIDGSHLPYDENVALCKKVVEYAHQFDVSVEGEL 150
                                               *99*999************************************************************** PP

                                 TIGR01859 136 GklgGieddvvekeaeladideakklvketgvDaLaiaiGtshGkykge.....pkldferlkeikkll 199
                                               G+l+Gied+v ++++++++++e++++vk+tgvD+Lai+iGtshG yk +     p l+f+ l+e +k+l
  lcl|NCBI__GCF_000020385.1:WP_012469022.1 151 GVLAGIEDEVSAEHSTYTKPEEVEDFVKKTGVDSLAISIGTSHGAYKFKagqpvPPLRFDILAECEKRL 219
                                               ********************************************88777779999************** PP

                                 TIGR01859 200 n.lPlvlhGas.....................Gipeeqlkkaiklgiakvnidtdlrlaftaairkvle 246
                                               + +P+vlhGas                     G+peeql++a+ ++++k+nid+d rla+ta++r+++ 
  lcl|NCBI__GCF_000020385.1:WP_012469022.1 220 PgFPIVLHGASsvvqeyvelinqnggkmegavGVPEEQLRQAAASAVCKINIDSDGRLAVTAKVREYFG 288
                                               99******************************************************************* PP

                                 TIGR01859 247 ekkdeydpRkilaparealkevvkekik.vlgsagka 282
                                               ++ +e+dpRk+l++ar++l +++k+k++ vlgsagka
  lcl|NCBI__GCF_000020385.1:WP_012469022.1 289 KDPKEFDPRKYLGEARKELIKLIKHKNEtVLGSAGKA 325
                                               **************************9989*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (325 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: 10.78
//
[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:

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