Alignments for a candidate for fba in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Rhodococcus qingshengii djl-6-2

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_007726777.1 C1M55_RS07165 class II fructose-bisphosphate aldolase

Query= BRENDA::P9WQA3
         (344 letters)



>NCBI__GCF_002893965.1:WP_007726777.1
          Length = 345

 Score =  577 bits (1488), Expect = e-169
 Identities = 281/343 (81%), Positives = 315/343 (91%)

Query: 1   MPIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFG 60
           MPIATPEVYAEMLG+AK++S+AFPAINC  SE++NAAIKGFADAGSDGIIQFSTGGAEFG
Sbjct: 1   MPIATPEVYAEMLGRAKEHSFAFPAINCVGSESINAAIKGFADAGSDGIIQFSTGGAEFG 60

Query: 61  SGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKG 120
           SGLGVKDMVTGAVALAEF HVIAAKY V +ALHTDHCPKDKLD+YVRPLLAIS +RV  G
Sbjct: 61  SGLGVKDMVTGAVALAEFAHVIAAKYDVTIALHTDHCPKDKLDTYVRPLLAISQERVDAG 120

Query: 121 GNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKL 180
            NPLFQSHMWDGSA+PIDENLAIA+ELL  + AA+IILE+EIGVVGGEEDGV  EIN+KL
Sbjct: 121 RNPLFQSHMWDGSAIPIDENLAIAKELLALSKAARIILEVEIGVVGGEEDGVEAEINDKL 180

Query: 181 YTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGL 240
           YTS EDFEKT++ALG GE GKYLLAATFGNVHGVYKPGNVKL+P++L +GQ+VAAAKLGL
Sbjct: 181 YTSSEDFEKTVDALGIGEQGKYLLAATFGNVHGVYKPGNVKLKPEVLEEGQKVAAAKLGL 240

Query: 241 PADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLK 300
            + ++PFDFVFHGGSGSLKSEIE++L +GVVKMNVDTDTQYAF+RPIAGH FTNYDGVLK
Sbjct: 241 ASGSQPFDFVFHGGSGSLKSEIEDSLNFGVVKMNVDTDTQYAFSRPIAGHFFTNYDGVLK 300

Query: 301 VDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLT 343
           VDGEVG KK YDPRSYLKKAEA M+ RVV+ACNDL  AG+S++
Sbjct: 301 VDGEVGNKKAYDPRSYLKKAEAGMTARVVEACNDLKSAGRSVS 343


Lambda     K      H
   0.316    0.133    0.384 

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: 452
Number of extensions: 9
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: 344
Length of database: 345
Length adjustment: 29
Effective length of query: 315
Effective length of database: 316
Effective search space:    99540
Effective search space used:    99540
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_007726777.1 C1M55_RS07165 (class II fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-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/TIGR01520.hmm
# target sequence database:        /tmp/gapView.1292868.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-146  473.6   0.2   2.1e-146  473.5   0.2    1.0  1  NCBI__GCF_002893965.1:WP_007726777.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_007726777.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.5   0.2  2.1e-146  2.1e-146       9     356 ..       3     340 ..       1     341 [. 0.99

  Alignments for each domain:
  == domain 1  score: 473.5 bits;  conditional E-value: 2.1e-146
                             TIGR01520   9 vilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaekaasi 81 
                                           ++++e++a++++ ake++fa+Pain+v+se++naa+++++da+s++i+qfs+gga+f +G+Gvkd      ++
  NCBI__GCF_002893965.1:WP_007726777.1   3 IATPEVYAEMLGRAKEHSFAFPAINCVGSESINAAIKGFADAGSDGIIQFSTGGAEFGSGLGVKD------MV 69 
                                           789**************************************************************......9* PP

                             TIGR01520  82 aGaiaaaeyvrsiaekygvpvvlhtdhCakkllp.yvdglleadekyfkkegkPlfsshmldlseepieenie 153
                                           +Ga+a+ae+ ++ia+ky v ++lhtdhC+k++l+ yv++ll+++++++ ++ +Plf+shm+d+s+ pi+en++
  NCBI__GCF_002893965.1:WP_007726777.1  70 TGAVALAEFAHVIAAKYDVTIALHTDHCPKDKLDtYVRPLLAISQERVDAGRNPLFQSHMWDGSAIPIDENLA 142
                                           ************************************************************************* PP

                             TIGR01520 154 iakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelsk.ispkfsiaaafGnvhG 225
                                           iak++l    ++ +ile+eiG++GGeedGv+ e +  ++lyt+ ed+ek++++l   +++k+ +aa+fGnvhG
  NCBI__GCF_002893965.1:WP_007726777.1 143 IAKELLALSKAARIILEVEIGVVGGEEDGVEAEIN--DKLYTSSEDFEKTVDALGIgEQGKYLLAATFGNVHG 213
                                           *********************************99..79***************9889*************** PP

                             TIGR01520 226 vykpGnvklrPdiladgqeyvaeklglke.akplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaaleg 297
                                           vykpGnvkl+P++l++gq+++a+klgl + ++p++fvfhGGsGs+k+ei+++l++Gvvk+nvdtdtqya+ ++
  NCBI__GCF_002893965.1:WP_007726777.1 214 VYKPGNVKLKPEVLEEGQKVAAAKLGLASgSQPFDFVFHGGSGSLKSEIEDSLNFGVVKMNVDTDTQYAFSRP 286
                                           ***************************9989****************************************** PP

                             TIGR01520 298 ildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                           i++++++n+d +++++G     e++nkk ydPr++l++ae+ m+arv++a+++l+++++
  NCBI__GCF_002893965.1:WP_007726777.1 287 IAGHFFTNYDGVLKVDG-----EVGNKKAYDPRSYLKKAEAGMTARVVEACNDLKSAGR 340
                                           *****************.....9*******************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (345 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.12
//
[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 2024 update 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