GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Magnetospirillum magneticum AMB-1

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011383790.1 AMB_RS06985 fructose-bisphosphate aldolase class II

Query= BRENDA::Q602L6
         (354 letters)



>NCBI__GCF_000009985.1:WP_011383790.1
          Length = 354

 Score =  523 bits (1347), Expect = e-153
 Identities = 255/353 (72%), Positives = 300/353 (84%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           M+L+S+RQLLDHAAE+ YG+PAFNVNNMEQ+KAIMEAASA DAPVILQ SAGAR YAGEP
Sbjct: 1   MSLVSMRQLLDHAAENSYGIPAFNVNNMEQVKAIMEAASACDAPVILQASAGARKYAGEP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE YP IPVCMHQDHG SPA+ +R+IQSGFSSVMMDGSL ED KTP+ + Y
Sbjct: 61  FLRHLILAAIEAYPQIPVCMHQDHGTSPAINVRAIQSGFSSVMMDGSLREDGKTPSDWDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++VV++AHACGVSVEGELGCLGSLETG AGKEDG GAEG+LDHS LLTDPDEAA+
Sbjct: 121 NVAVTKQVVDIAHACGVSVEGELGCLGSLETGTAGKEDGVGAEGKLDHSQLLTDPDEAAE 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV+ TQVDALAIAIGTSHGAYKFTR PTG+VL I R+K IH RIP  HLVMHGSSSVP++
Sbjct: 181 FVKLTQVDALAIAIGTSHGAYKFTRPPTGEVLAIKRIKEIHARIPNTHLVMHGSSSVPQD 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
             +++NDYGG +G+TYGVPV EIVEGI+HGVRK+NIDTDLR+A  G +R++  ++ K FD
Sbjct: 241 LLKIVNDYGGALGETYGVPVGEIVEGIKHGVRKINIDTDLRLAVTGCIRKYFHDNPKKFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIV 353
           PR   K +  AM  +C++RY+AFG +GQA+KIK + LEDMS  YA+G L P V
Sbjct: 301 PRDYLKPSIAAMVEVCKSRYDAFGTSGQASKIKVVGLEDMSALYAKGALAPKV 353


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: 21
Number of successful extensions: 2
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: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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 WP_011383790.1 AMB_RS06985 (fructose-bisphosphate aldolase class II)
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.8180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-198  643.6   0.2   4.3e-198  643.4   0.2    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383790.1  AMB_RS06985 fructose-bisphosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383790.1  AMB_RS06985 fructose-bisphosphate aldolase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.4   0.2  4.3e-198  4.3e-198       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 643.4 bits;  conditional E-value: 4.3e-198
                                 TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 
                                               l+s+rqlldhaae++yg+pafnvnn+eq++aimeaa ++d+pvilqas+gar+yage++lr+l+laa+e
  lcl|NCBI__GCF_000009985.1:WP_011383790.1   3 LVSMRQLLDHAAENSYGIPAFNVNNMEQVKAIMEAASACDAPVILQASAGARKYAGEPFLRHLILAAIE 71 
                                               69******************************************************************* PP

                                 TIGR01521  70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138
                                                yp+ipv++hqdhg+spa+  +aiq gf+svmmdgsl+ed+ktp+d+dynv vt++vv +aha+g+sve
  lcl|NCBI__GCF_000009985.1:WP_011383790.1  72 AYPQIPVCMHQDHGTSPAINVRAIQSGFSSVMMDGSLREDGKTPSDWDYNVAVTKQVVDIAHACGVSVE 140
                                               ********************************************************************* PP

                                 TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207
                                               gelgclgsletg++++edg+g+eg+ld+sqlltdp+eaaefvk t+vdala+aigtshgaykftr+ptg
  lcl|NCBI__GCF_000009985.1:WP_011383790.1 141 GELGCLGSLETGTAGKEDGVGAEGKLDHSQLLTDPDEAAEFVKLTQVDALAIAIGTSHGAYKFTRPPTG 209
                                               ********************************************************************* PP

                                 TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276
                                               evlai+ri+eih+r+p+thlvmhgsssvpq+ l+++n+ygg++ etygvpv eiv+gik+gvrk+nidt
  lcl|NCBI__GCF_000009985.1:WP_011383790.1 210 EVLAIKRIKEIHARIPNTHLVMHGSSSVPQDLLKIVNDYGGALGETYGVPVGEIVEGIKHGVRKINIDT 278
                                               ********************************************************************* PP

                                 TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345
                                               dlrla+t+ +r+   ++p++fdpr +lk+++ am +vck+ry+afgt+g+askikvv le+m + yakg
  lcl|NCBI__GCF_000009985.1:WP_011383790.1 279 DLRLAVTGCIRKYFHDNPKKFDPRDYLKPSIAAMVEVCKSRYDAFGTSGQASKIKVVGLEDMSALYAKG 347
                                               ********************************************************************* PP

                                 TIGR01521 346 el 347
                                                l
  lcl|NCBI__GCF_000009985.1:WP_011383790.1 348 AL 349
                                               86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 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: 6.29
//
[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