Alignments for a candidate for fba in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Shewanella oneidensis MR-1

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 200117 SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__MR1:200117
          Length = 355

 Score =  512 bits (1318), Expect = e-150
 Identities = 251/351 (71%), Positives = 286/351 (81%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALISLRQLLDHAAEHGYG+PAFNVNN+EQ++AIM+AA A D+PVI+Q SAGAR YA   
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FL++L+ AA+E YP IPVC+HQDHG  P +C RSIQ G SSVMMDGSL+ D KTPASY Y
Sbjct: 61  FLKYLMTAALEQYPDIPVCIHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TR+ V  AHACGVSVEGE+GCLGSLETG AG+EDG GAEG L H  LLT P+EAA 
Sbjct: 121 NVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGVGAEGVLSHDQLLTSPEEAAR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV  T VDALAIAIGTSHGAYKF+RKPTG VLRIDR+K IH RIP  HLVMHGSSSVP+E
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN YGG I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+++ E    FD
Sbjct: 241 WLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDP 351
           PRK  KA+  AM  IC  RYEAFG AGQA+KIKPL L+ M  AY  G LDP
Sbjct: 301 PRKFLKASMEAMADICTVRYEAFGCAGQASKIKPLSLQAMYKAYQSGALDP 351


Lambda     K      H
   0.320    0.134    0.391 

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: 507
Number of extensions: 15
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: 355
Length adjustment: 29
Effective length of query: 325
Effective length of database: 326
Effective search space:   105950
Effective search space used:   105950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 200117 SO0933 (fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file))
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.6336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.9e-196  638.0   0.1   2.2e-196  637.8   0.1    1.0  1  lcl|FitnessBrowser__MR1:200117  SO0933 fructose-bisphosphate ald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200117  SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.8   0.1  2.2e-196  2.2e-196       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 637.8 bits;  conditional E-value: 2.2e-196
                       TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvvlh 79 
                                     lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya  ++l+ l+ aa e+ypdipv++h
  lcl|FitnessBrowser__MR1:200117   3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMTAALEQYPDIPVCIH 81 
                                     69***************************************************************************** PP

                       TIGR01521  80 qdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgeaedgh 158
                                     qdhg++p++c+++iqlg++svmmdgsl +d+ktpa+y+ynv+vt ++v++aha+g+svege+gclgsletg++++edg+
  lcl|FitnessBrowser__MR1:200117  82 QDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEYNVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGV 160
                                     ******************************************************************************* PP

                       TIGR01521 159 gfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhgsssvpq 237
                                     g+eg+l + qllt peeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhgsssvpq
  lcl|FitnessBrowser__MR1:200117 161 GAEGVLSHDQLLTSPEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQ 239
                                     ******************************************************************************* PP

                       TIGR01521 238 ewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvcka 316
                                     ewl++in+ygg+i+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+ +a++psefdprkflk ++eam d+c+ 
  lcl|FitnessBrowser__MR1:200117 240 EWLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFDPRKFLKASMEAMADICTV 318
                                     ******************************************************************************* PP

                       TIGR01521 317 ryeafgtagnaskikvvsleemarryakgel 347
                                     ryeafg ag+askik++sl+ m++ y +g l
  lcl|FitnessBrowser__MR1:200117 319 RYEAFGCAGQASKIKPLSLQAMYKAYQSGAL 349
                                     ***************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (355 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: 9.74
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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