GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fba in Klebsiella michiganensis M5al

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate BWI76_RS23975 BWI76_RS23975 class II fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS23975 BWI76_RS23975 class II
           fructose-bisphosphate aldolase
          Length = 359

 Score =  695 bits (1794), Expect = 0.0
 Identities = 337/359 (93%), Positives = 350/359 (97%)

Query: 1   MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60
           MSKIFDFVKPGVITGDDVQKVFQVAKEN FALPAVNCVGTDSINAVLE AAKV++PVIVQ
Sbjct: 1   MSKIFDFVKPGVITGDDVQKVFQVAKENQFALPAVNCVGTDSINAVLEAAAKVRSPVIVQ 60

Query: 61  FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120
           FSNGGA+FIAGKGVK+DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI
Sbjct: 61  FSNGGAAFIAGKGVKTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120

Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180
           DGLLDAGEKHFAATGKPLFSSHMIDLSEESL ENIEICSKYL RM+K+ MTLEIELGCTG
Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLHENIEICSKYLARMAKMDMTLEIELGCTG 180

Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240
           GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT
Sbjct: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240

Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300
           ILRDSQEYVSKKHNLPHNSLNFVFHGGSGS+AQEIKDSVSYGV+KMNIDTDTQWATW+G+
Sbjct: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSSAQEIKDSVSYGVIKMNIDTDTQWATWDGI 300

Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359
           L YYK NEAYLQGQLGNPKGEDQPNKKYYDPRVWLRA QTSM+ RLE+AF+ELNAIDVL
Sbjct: 301 LQYYKTNEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAAQTSMVTRLEQAFKELNAIDVL 359


Lambda     K      H
   0.316    0.133    0.392 

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: 583
Number of extensions: 5
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: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
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 BWI76_RS23975 BWI76_RS23975 (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.18471.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     1e-195  635.7   0.3   1.1e-195  635.5   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23975  BWI76_RS23975 class II fructose-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23975  BWI76_RS23975 class II fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  635.5   0.3  1.1e-195  1.1e-195       1     356 [.       4     358 ..       4     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 635.5 bits;  conditional E-value: 1.1e-195
                               TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGv 71 
                                             ++d++k+gvi+g+dv+k+f+vake++fa+Pa+n+v+++++na+leaa++++sp+i+qfsnggaafiaGkGv
  lcl|FitnessBrowser__Koxy:BWI76_RS23975   4 IFDFVKPGVITGDDVQKVFQVAKENQFALPAVNCVGTDSINAVLEAAAKVRSPVIVQFSNGGAAFIAGKGV 74 
                                             6899******************************************************************* PP

                               TIGR01520  72 kdeaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmld 142
                                             k++++++a+i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+d
  lcl|FitnessBrowser__Koxy:BWI76_RS23975  75 KTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMID 145
                                             *********************************************************************** PP

                               TIGR01520 143 lseepieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispk 213
                                             lsee+++eniei++kyl rmak++++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y+elskisp+
  lcl|FitnessBrowser__Koxy:BWI76_RS23975 146 LSEESLHENIEICSKYLARMAKMDMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPR 216
                                             *********************************************************************** PP

                               TIGR01520 214 fsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkv 284
                                             f+iaa+fGnvhGvykpGnv+l+P+il+d+qeyv++k++l+ +++l+fvfhGGsGs+++eik+++syGv+k+
  lcl|FitnessBrowser__Koxy:BWI76_RS23975 217 FTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVSKKHNLP-HNSLNFVFHGGSGSSAQEIKDSVSYGVIKM 286
                                             ****************************************.9***************************** PP

                               TIGR01520 285 nvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnain 355
                                             n+dtdtq+a++ gil+y+++ne+ylq+q+Gnpkge++pnkk+ydPrvwlr+a++sm  r+e+a++elnai+
  lcl|FitnessBrowser__Koxy:BWI76_RS23975 287 NIDTDTQWATWDGILQYYKTNEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAAQTSMVTRLEQAFKELNAID 357
                                             *********************************************************************98 PP

                               TIGR01520 356 k 356
                                             +
  lcl|FitnessBrowser__Koxy:BWI76_RS23975 358 V 358
                                             6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (359 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: 7.06
//
[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:

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:

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:

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, or view the source code.

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