Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03264 H281DRAFT_03264 methylmalonate-semialdehyde dehydrogenase [acylating]

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Burk376:H281DRAFT_03264
          Length = 507

 Score =  604 bits (1557), Expect = e-177
 Identities = 303/493 (61%), Positives = 375/493 (76%), Gaps = 4/493 (0%)

Query: 4   IKHLIGGELIAD-TGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           I H IGG  +   +GR  +VFNP+TG+    V LA  E +  A+ +AKAAF AW  T P 
Sbjct: 15  IGHYIGGVAVDPASGRFKEVFNPATGQVTGAVALASIEEVDAAVQSAKAAFAAWSETAPL 74

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           KRA++LF+FK+LL  + + +  LI+ EHGK   DA GE+ RGIE VE+A   P +LK ++
Sbjct: 75  KRARILFKFKELLNKHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDF 134

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           +  +G  ID W+  QP+GVVAGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS++L
Sbjct: 135 TDQIGGGIDNWNLRQPLGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASL 194

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
            IAEL  EAGLP GV NVV+GDK AVDALIE P+V ALSFVGSTPIAEYI++E +KRGKR
Sbjct: 195 RIAELLKEAGLPDGVFNVVNGDKVAVDALIEHPDVAALSFVGSTPIAEYIHTEASKRGKR 254

Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302
           VQALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VG+ +AD L++KLV
Sbjct: 255 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGN-VADKLIEKLV 313

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362
           P++K L I  G +   +MGPLVT   + KV GYI +G  +GA L+VDGR + VA +E GF
Sbjct: 314 PRVKSLVIKNGENLDAEMGPLVTAEHKAKVAGYIASGEEEGATLIVDGRAHPVA-NEAGF 372

Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422
           F+GGTLFD V  +M IYKEEIFGPVL +VRV     A++LIN HE+GNG  +FT DG  A
Sbjct: 373 FIGGTLFDNVGTQMKIYKEEIFGPVLAVVRVPDFASAVELINAHEFGNGVSLFTSDGGVA 432

Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWP 482
           R F  +I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +GVRFYT+ K+I QRWP
Sbjct: 433 RAFGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWP 492

Query: 483 QRKSHEAAQFAFP 495
              + + A+F  P
Sbjct: 493 DSIA-KGAEFTMP 504


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: 788
Number of extensions: 30
Number of successful extensions: 3
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: 507
Length adjustment: 34
Effective length of query: 464
Effective length of database: 473
Effective search space:   219472
Effective search space used:   219472
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 H281DRAFT_03264 H281DRAFT_03264 (methylmalonate-semialdehyde dehydrogenase [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.10022.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.3e-214  698.4   2.4   2.7e-214  698.2   2.4    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03264  H281DRAFT_03264 methylmalonate-s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03264  H281DRAFT_03264 methylmalonate-semialdehyde dehydrogenase [acylating]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.2   2.4  2.7e-214  2.7e-214       2     477 .]      16     491 ..      15     491 .. 0.99

  Alignments for each domain:
  == domain 1  score: 698.2 bits;  conditional E-value: 2.7e-214
                                    TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvll 67 
                                                   h+i+G  v+ +s+++ +v npat++v++ va as eevdaav sa+ +faaw+et+ ++rar+l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264  16 GHYIGGVAVDPASGRFKEVFNPATGQVTGAVALASIEEVDAAVQSAKAAFAAWSETAPLKRARILF 81 
                                                  59**************************************************************** PP

                                    TIGR01722  68 ryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysi 133
                                                  ++++ll++h+de+a li+ e+Gk+++da+G+v+rG+evve+ac+++ ll+ + ++++   +d + +
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264  82 KFKELLNKHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTDQIGGGIDNWNL 147
                                                  ****************************************************************** PP

                                    TIGR01722 134 rqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvv 199
                                                  rqplGvvaGitpfnfp m+p+wmfp+a+acGntfvlkpse++psa++++aell+eaG+pdGv+nvv
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 148 RQPLGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRIAELLKEAGLPDGVFNVV 213
                                                  ****************************************************************** PP

                                    TIGR01722 200 hGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaalda 265
                                                   Gdk+avd l+ehpdv a+sfvGs++++eyi++ +s++gkrvqal+Gaknh vv+pdad+++a+da
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 214 NGDKVAVDALIEHPDVAALSFVGSTPIAEYIHTEASKRGKRVQALGGAKNHLVVMPDADLDQAVDA 279
                                                  ****************************************************************** PP

                                    TIGR01722 266 lvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervas 330
                                                  l+gaa+G+aG+rcmais+av+vG++ ++l+e+++ r++ + +  g++  ae+Gpl+t ++k++va 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 280 LIGAAYGSAGERCMAISVAVAVGNVaDKLIEKLVPRVKSLVIKNGENLDAEMGPLVTAEHKAKVAG 345
                                                  ************************989*************************************** PP

                                    TIGR01722 331 liasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeai 396
                                                  +iasg +eGa +++dGr+  v   e G f+G tl+++v ++mkiykeeifGpvl+v+++  +  a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 346 YIASGEEEGATLIVDGRAHPVA-NEAGFFIGGTLFDNVGTQMKIYKEEIFGPVLAVVRVPDFASAV 410
                                                  ********************96.699**************************************** PP

                                    TIGR01722 397 klinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkq 462
                                                  +lin+  +GnG ++ftsdG+ ar f  +i+vG+vG+nvpipvp++++sf+Gwk slfGd+h+yG++
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 411 ELINAHEFGNGVSLFTSDGGVARAFGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEE 476
                                                  ****************************************************************** PP

                                    TIGR01722 463 Gvrfytrlktvtarw 477
                                                  Gvrfytr k +  rw
  lcl|FitnessBrowser__Burk376:H281DRAFT_03264 477 GVRFYTRYKSIMQRW 491
                                                  **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (507 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: 00:00:00.03
# Mc/sec: 7.73
//
[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