GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Shewanella loihica PV-4

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__PV4:5208453
          Length = 496

 Score =  619 bits (1595), Expect = 0.0
 Identities = 303/496 (61%), Positives = 373/496 (75%), Gaps = 2/496 (0%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M  I H I G+    + R+A VF P+TGE    V LA    +  AI+ AK A   W    
Sbjct: 1   MQQINHYINGQHTQPSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMT 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           P  RA++LF+FK L+EAN + +  +I+ EHGK ++DA GE+ RG+E VE+A   P +LKG
Sbjct: 61  PLNRARILFKFKALVEANMDELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           E++  VG  +DAW+  Q +GVVAGI PFNFP MVP+WM+P+AIA GNTFI+KPSE+DP+S
Sbjct: 121 EHTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
            + +AEL  EAGLP GV NVV+GDK AVD L+   +++A+SFVGSTPIAEYIY      G
Sbjct: 181 VMRMAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNH +LMPDADLD AVSALMGAAYGS GERCMAISV + VG ++ DALV+K
Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVG-EVGDALVEK 299

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L+PQI+ LK+G G    ++MGPL++    DKV  Y+DTGV++GA L+ DGR   VA HE 
Sbjct: 300 LLPQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQ 359

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           G+FLGG LFD VTPEMTIYKEEIFGPVL IVRV    EA+ LIN+HE+GNGT IFT+ GE
Sbjct: 360 GYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGE 419

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AAR FC  ++VGMVGVNVP+PVP+A+HSFGGWKRSLFG LH +GPDGVRFYTKRKAIT R
Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479

Query: 481 WPQRKSHEAAQFAFPS 496
           WP+ K  + A+F  P+
Sbjct: 480 WPKGKGSQ-AEFVMPT 494


Lambda     K      H
   0.319    0.137    0.411 

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: 746
Number of extensions: 19
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: 498
Length of database: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate 5208453 Shew_0965 (methylmalonate-semialdehyde dehydrogenase (RefSeq))
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.30522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.2e-206  672.0   0.5   2.5e-206  671.9   0.5    1.0  1  lcl|FitnessBrowser__PV4:5208453  Shew_0965 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208453  Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.9   0.5  2.5e-206  2.5e-206       1     477 []       4     480 ..       4     480 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.9 bits;  conditional E-value: 2.5e-206
                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                      ++h+i+G+  +  s++   v +pat+e  a+v+ asa evdaa+  a++++  w+e + ++rar+l++++al++++ d
  lcl|FitnessBrowser__PV4:5208453   4 INHYINGQHTQ-PSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMTPLNRARILFKFKALVEANMD 80 
                                      689****9876.5789999*********************************************************** PP

                        TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwm 156
                                      e+a +i+ e+Gk+l+dakG+++rGlevve+ac+++ ll+Ge +e+v   vd ++++q lGvvaGi+pfnfp m+p+wm
  lcl|FitnessBrowser__PV4:5208453  81 ELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKGEHTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWM 158
                                      ****************************************************************************** PP

                        TIGR01722 157 fplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetg 234
                                      fp+aia Gntf++kpsek+p++ +++aell+eaG+pdGv+nvv Gdkeavd+ll h d++avsfvGs++++eyiy+t+
  lcl|FitnessBrowser__PV4:5208453 159 FPIAIAAGNTFIMKPSEKDPTSVMRMAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTA 236
                                      ****************************************************************************** PP

                        TIGR01722 235 sahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagdd 311
                                      +ahgkrvqal+Gaknhm+++pdad+++a++al+gaa+G+aG+rcmais++++vG++ + lve++  +++ ++vg g +
  lcl|FitnessBrowser__PV4:5208453 237 AAHGKRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVgDALVEKLLPQIQALKVGNGLE 314
                                      ********************************************************999******************* PP

                        TIGR01722 312 pgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlea 389
                                         e+Gpli+ q+ ++v s++++g+ eGa++l dGr ++v  +e+G f+G +l+++v p+m+iykeeifGpvl+++++
  lcl|FitnessBrowser__PV4:5208453 315 GEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQGYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRV 392
                                      ****************************************************************************** PP

                        TIGR01722 390 dtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfy 467
                                        + ea+ line  +GnGtaift++G aar+f h+++vG+vGvnvpipvp++f+sf+Gwk slfG lh++G +Gvrfy
  lcl|FitnessBrowser__PV4:5208453 393 KDYAEALTLINEHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFY 470
                                      ****************************************************************************** PP

                        TIGR01722 468 trlktvtarw 477
                                      t+ k++tarw
  lcl|FitnessBrowser__PV4:5208453 471 TKRKAITARW 480
                                      ********** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (496 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.83
//
[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:

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