Alignments for a candidate for fba in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Pedobacter sp. GW460-11-11-14-LB5

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate CA265_RS13135 CA265_RS13135 class II fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>FitnessBrowser__Pedo557:CA265_RS13135
          Length = 359

 Score =  495 bits (1275), Expect = e-145
 Identities = 235/349 (67%), Positives = 290/349 (83%), Gaps = 2/349 (0%)

Query: 11  GVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIA 70
           GVI GD VQ++F+ AK++ FALPAVN  GT+++NAVLETA  V +PV++Q SNGGA F A
Sbjct: 8   GVIYGDAVQELFEQAKKHQFALPAVNVTGTNTVNAVLETAKAVNSPVMIQLSNGGAQFYA 67

Query: 71  GKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKH 130
           GK + ++  Q A ILGA+S A HVH +AEHYGV V+LHTDH AKKLLPWIDGLLD GEK 
Sbjct: 68  GKSLDNEKLQ-ACILGAVSAAKHVHLLAEHYGVAVVLHTDHAAKKLLPWIDGLLDHGEKF 126

Query: 131 FAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVDNSH 190
           FA TGKPLFSSHM+DLSEES++EN+EI +KYL RM+K+ MT+EIELG TGGEEDGVDNS 
Sbjct: 127 FAETGKPLFSSHMLDLSEESIEENMEISAKYLARMAKMNMTIEIELGVTGGEEDGVDNSD 186

Query: 191 MDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRDSQEYVS 250
           +D+S LYTQP +V YAY ELSK+SPRFT+AA+FGNVHGVYKPGNV L P IL++SQ+++ 
Sbjct: 187 VDSSKLYTQPSEVAYAYEELSKVSPRFTVAAAFGNVHGVYKPGNVKLQPVILKNSQDFIK 246

Query: 251 KKHNL-PHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEA 309
           +K +L     +NFVFHGGSGST +EI++++SYG +KMNIDTD QWA WEG+L YYK NEA
Sbjct: 247 EKFSLTAEKPINFVFHGGSGSTQEEIREAISYGAIKMNIDTDMQWAFWEGILEYYKKNEA 306

Query: 310 YLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDV 358
           YLQGQ+GNP G+D+PNKKYYDPRVWLR G+ + + RL  AF++LN I+V
Sbjct: 307 YLQGQIGNPDGDDKPNKKYYDPRVWLRKGEETFVKRLTTAFEDLNCINV 355


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: 431
Number of extensions: 14
Number of successful extensions: 3
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 CA265_RS13135 CA265_RS13135 (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.2703.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.7e-178  577.6   1.2   5.7e-178  577.3   1.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS13135  CA265_RS13135 class II fructose-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS13135  CA265_RS13135 class II fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.3   1.2  5.7e-178  5.7e-178       7     356 ..       7     355 ..       2     356 .. 0.99

  Alignments for each domain:
  == domain 1  score: 577.3 bits;  conditional E-value: 5.7e-178
                                  TIGR01520   7 tgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkde 74 
                                                 gvi+g+ v++lfe+ak+++fa+Pa+nv++++tvna+le+a+ ++sp+++q+sngga+f+aGk + +e
  lcl|FitnessBrowser__Pedo557:CA265_RS13135   7 KGVIYGDAVQELFEQAKKHQFALPAVNVTGTNTVNAVLETAKAVNSPVMIQLSNGGAQFYAGKSLDNE 74 
                                                58****************************************************************** PP

                                  TIGR01520  75 aekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmld 142
                                                + +a  i Ga++aa++v+ +ae+ygv vvlhtdh akkllp++dgll+++ek+f+++gkPlfsshmld
  lcl|FitnessBrowser__Pedo557:CA265_RS13135  75 KLQA-CILGAVSAAKHVHLLAEHYGVAVVLHTDHAAKKLLPWIDGLLDHGEKFFAETGKPLFSSHMLD 141
                                                *999.9************************************************************** PP

                                  TIGR01520 143 lseepieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelski 210
                                                lsee+ieen+ei+ kyl rmak+++++eie+G+tGGeedGvdn+++d+++lyt+P +v ++yeelsk+
  lcl|FitnessBrowser__Pedo557:CA265_RS13135 142 LSEESIEENMEISAKYLARMAKMNMTIEIELGVTGGEEDGVDNSDVDSSKLYTQPSEVAYAYEELSKV 209
                                                ******************************************************************** PP

                                  TIGR01520 211 spkfsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikeals 278
                                                sp+f++aaafGnvhGvykpGnvkl+P il+++q++++ek +l ++kp++fvfhGGsGst+eei+ea+s
  lcl|FitnessBrowser__Pedo557:CA265_RS13135 210 SPRFTVAAAFGNVHGVYKPGNVKLQPVILKNSQDFIKEKFSLTAEKPINFVFHGGSGSTQEEIREAIS 277
                                                ******************************************************************** PP

                                  TIGR01520 279 yGvvkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvek 346
                                                yG +k+n+dtd+q+a++egil+y++kne+ylq+q+Gnp+g +kpnkk+ydPrvwlr++e++  +r+++
  lcl|FitnessBrowser__Pedo557:CA265_RS13135 278 YGAIKMNIDTDMQWAFWEGILEYYKKNEAYLQGQIGNPDGDDKPNKKYYDPRVWLRKGEETFVKRLTT 345
                                                ******************************************************************** PP

                                  TIGR01520 347 aleelnaink 356
                                                a+e+ln+in+
  lcl|FitnessBrowser__Pedo557:CA265_RS13135 346 AFEDLNCINV 355
                                                ********97 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: 8.91
//
[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