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

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.27696.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: 11.13
//
[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