GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Shewanella sp. ANA-3

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 7026208 Shewana3_3350 fructose-1,6-bisphosphate aldolase (RefSeq)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__ANA3:7026208
          Length = 355

 Score =  513 bits (1322), Expect = e-150
 Identities = 252/351 (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 Q+IN YGG I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+++ E    FD
Sbjct: 241 WLQIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFD 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: 506
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 7026208 Shewana3_3350 (fructose-1,6-bisphosphate aldolase (RefSeq))
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.3052518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-196  638.2   0.2   1.8e-196  638.1   0.2    1.0  1  lcl|FitnessBrowser__ANA3:7026208  Shewana3_3350 fructose-1,6-bisph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026208  Shewana3_3350 fructose-1,6-bisphosphate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  638.1   0.2  1.8e-196  1.8e-196       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 638.1 bits;  conditional E-value: 1.8e-196
                         TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvv 77 
                                       lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya  ++l+ l+ aa e+ypdipv+
  lcl|FitnessBrowser__ANA3:7026208   3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMTAALEQYPDIPVC 79 
                                       69*************************************************************************** PP

                         TIGR01521  78 lhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgea 154
                                       +hqdhg++p++c+++iqlg++svmmdgsl +d+ktpa+y+ynv+vt ++v++aha+g+svege+gclgsletg++++
  lcl|FitnessBrowser__ANA3:7026208  80 IHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEYNVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGE 156
                                       ***************************************************************************** PP

                         TIGR01521 155 edghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhg 231
                                       edg+g+eg+l + qllt peeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhg
  lcl|FitnessBrowser__ANA3:7026208 157 EDGVGAEGVLSHDQLLTSPEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHG 233
                                       ***************************************************************************** PP

                         TIGR01521 232 sssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkave 308
                                       sssvpqewl++in+ygg+i+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+ +a++psefdprkflk ++e
  lcl|FitnessBrowser__ANA3:7026208 234 SSSVPQEWLQIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFDPRKFLKASME 310
                                       ***************************************************************************** PP

                         TIGR01521 309 amkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                       am d+c+ ryeafg ag+askik++sl+ m++ y +g l
  lcl|FitnessBrowser__ANA3:7026208 311 AMADICTVRYEAFGCAGQASKIKPLSLQAMYKAYQSGAL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.77
//
[ok]

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

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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:

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