Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS02840 BWI76_RS02840 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::Koxy:BWI76_RS03070
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS02840
          Length = 503

 Score =  458 bits (1179), Expect = e-133
 Identities = 229/480 (47%), Positives = 317/480 (66%), Gaps = 5/480 (1%)

Query: 7   FIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTTPLRRA 66
           F+ G+   S + + M V++P+TG+V+ +    T QEV DA+  AR AF +WS T  ++R+
Sbjct: 10  FVDGQWRVSQTERYMDVYNPSTGEVMAQAPCCTEQEVLDAVAAARKAFPAWSDTPAIKRS 69

Query: 67  RVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKGEFSSD 126
           ++MF  + LL QH + L  ++  E+GK + DA G++ +  E  E AC IP L+ GE   D
Sbjct: 70  QIMFRVRELLIQHQDRLTELVAKENGKAWGDAQGDVLKAKEGTELACSIPTLMAGENLMD 129

Query: 127 VGTGVDSYSLMQPLGVVAGITPFNFPAMVPM-WMFPLALACGNSFVLKPPALAPTAAVRL 185
              G+D+    +P+GV AGI PFNFPAM+PM WM PL +A GN+ V+K  ++ P   + +
Sbjct: 130 ASAGIDTNLYREPIGVFAGIVPFNFPAMIPMGWMAPLCVASGNTMVIKAASMTPMTCMEI 189

Query: 186 AELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAYGKRVQ 245
            +L +EAG+PDGV NVV CS  +A+ L   P +  VSFVGS+ V  H+Y  A+A+GKRVQ
Sbjct: 190 TKLYQEAGVPDGVINVVTCSRNEADILLTHPDVNGVSFVGSTSVGLHVYSKAAAHGKRVQ 249

Query: 246 AFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIARLKPL 305
           A   AKNHA+V+ DA ++ T   I+  AFG AGERCMALPVVV V +E ADKLIA +   
Sbjct: 250 ALCEAKNHALVLADAPINRTAAGIINAAFGCAGERCMALPVVV-VQEEIADKLIAAVVEK 308

Query: 306 VESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVPGFEEG 365
            + LK+GPG +R   + +MGPV+S  H++ V+G+I+KG+ EGA LV+DGR  +VPG E G
Sbjct: 309 AKQLKIGPGYLR---DTDMGPVISKDHKRSVIGWINKGIEEGAKLVLDGRDIKVPGQENG 365

Query: 366 YYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFTSNGHT 425
           +YVG T+ D VT EM++  +EIFGPVL   RV  +   L+L+N++ F NGS +FT +G+ 
Sbjct: 366 FYVGPTILDRVTEEMSVGTQEIFGPVLCFKRVKTFEEGLQLMNNNPFANGSVIFTQSGYY 425

Query: 426 AREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTATVRW 485
           AREF      GMVG+NV +PVP+    F G K+S FG L+  G DGVRFYT  K  T RW
Sbjct: 426 AREFQKRTHGGMVGINVGIPVPVGVFPFSGHKQSFFGDLHCLGKDGVRFYTESKCVTSRW 485


Lambda     K      H
   0.319    0.135    0.404 

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: 616
Number of extensions: 21
Number of successful extensions: 4
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: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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: 52 (24.6 bits)

Align candidate BWI76_RS02840 BWI76_RS02840 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.2101578.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.2e-176  572.6   0.7   3.6e-176  572.4   0.7    1.0  1  FitnessBrowser__Koxy:BWI76_RS02840  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS02840  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.4   0.7  3.6e-176  3.6e-176       2     477 .]       8     485 ..       7     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 572.4 bits;  conditional E-value: 3.6e-176
                           TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkeh 76 
                                         k+++dG+   +++++y++v np t+ev+a+ ++++ +ev  ava+ar++f+aw++t+  +r+++++r ++ll +h
  FitnessBrowser__Koxy:BWI76_RS02840   8 KYFVDGQWRVSQTERYMDVYNPSTGEVMAQAPCCTEQEVLDAVAAARKAFPAWSDTPAIKRSQIMFRVRELLIQH 82 
                                         79************************************************************************* PP

                           TIGR01722  77 rdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpam 151
                                         +d +++l++ e+Gk++ da+Gdv++  e  e+acs+++l+ Ge   + +  +d+  +r p+Gv aGi pfnfpam
  FitnessBrowser__Koxy:BWI76_RS02840  83 QDRLTELVAKENGKAWGDAQGDVLKAKEGTELACSIPTLMAGENLMDASAGIDTNLYREPIGVFAGIVPFNFPAM 157
                                         *************************************************************************** PP

                           TIGR01722 152 ipl.wmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsva 225
                                         ip+ wm pl +a Gnt+v+k +   p +++++++l++eaG+pdGv+nvv   +++ d ll hpdv  vsfvGs++
  FitnessBrowser__Koxy:BWI76_RS02840 158 IPMgWMAPLCVASGNTMVIKAASMTPMTCMEITKLYQEAGVPDGVINVVTCSRNEADILLTHPDVNGVSFVGSTS 232
                                         **99*********************************************************************** PP

                           TIGR01722 226 vgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeire 299
                                         vg ++y++++ahgkrvqal  aknh++vl da  ++++  +++aa+G+aG+rcma+ ++v+  ++ ++l+  ++e
  FitnessBrowser__Koxy:BWI76_RS02840 233 VGLHVYSKAAAHGKRVQALCEAKNHALVLADAPINRTAAGIINAAFGCAGERCMALPVVVVQEEIaDKLIAAVVE 307
                                         **********************************************************99999877********* PP

                           TIGR01722 300 raekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmki 374
                                         +a+++++g+g    +++Gp+i+k++k  v  +i++g++eGa+++ldGr +kv G e+G +vG+t+l+rv  +m++
  FitnessBrowser__Koxy:BWI76_RS02840 308 KAKQLKIGPGYLRDTDMGPVISKDHKRSVIGWINKGIEEGAKLVLDGRDIKVPGQENGFYVGPTILDRVTEEMSV 382
                                         *************************************************************************** PP

                           TIGR01722 375 ykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwk 449
                                           +eifGpvl+  ++ t+ee+++l+n++p+ nG+ ift++G  ar+fq++ + G+vG+nv ipvp+++f f+G+k
  FitnessBrowser__Koxy:BWI76_RS02840 383 GTQEIFGPVLCFKRVKTFEEGLQLMNNNPFANGSVIFTQSGYYAREFQKRTHGGMVGINVGIPVPVGVFPFSGHK 457
                                         *************************************************************************** PP

                           TIGR01722 450 dslfGdlhiyGkqGvrfytrlktvtarw 477
                                         +s+fGdlh  Gk+Gvrfyt++k vt+rw
  FitnessBrowser__Koxy:BWI76_RS02840 458 QSFFGDLHCLGKDGVRFYTESKCVTSRW 485
                                         **************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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: 22.16
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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