Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

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 RR42_RS01580 RR42_RS01580 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Cup4G11:RR42_RS01580
          Length = 505

 Score =  627 bits (1616), Expect = 0.0
 Identities = 309/493 (62%), Positives = 378/493 (76%), Gaps = 3/493 (0%)

Query: 4   IKHLIGGEL-IADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           I H IGG +  A + R ADVFNP+TG    +V L   + +  A+ AA AAFPAW  T P 
Sbjct: 12  IAHYIGGTVRAASSDRFADVFNPATGAVAGRVALGSAQDVDAAVAAAHAAFPAWSETAPL 71

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           KRA++LF+FK+LL+ + + +  LI+ EHGK   DA GE+ RG+E VE+A   P +LK ++
Sbjct: 72  KRARILFKFKELLDRHHDDLAALITREHGKVFSDAKGEVTRGVEIVEFACGIPNLLKTDF 131

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           + N+G  ID W+  QP+GVVAGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS +L
Sbjct: 132 TDNIGGGIDNWNLRQPLGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSPSL 191

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
           LIA+L  +AGLP GV NVV G K AVDAL+   +V+ALSFVGSTPIAEYIY+EGT+RGKR
Sbjct: 192 LIADLLKQAGLPDGVFNVVQGGKEAVDALLAHKDVQALSFVGSTPIAEYIYTEGTRRGKR 251

Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302
           VQALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VGD +AD LV +L 
Sbjct: 252 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGD-VADKLVPRLA 310

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362
            + + LKI  G     +MGPLVT A + KV GYI  GV +GA+LV DGRG+KV GHENGF
Sbjct: 311 ERARSLKIRNGMQDDAEMGPLVTAAHKAKVEGYIAKGVEEGAKLVTDGRGHKVDGHENGF 370

Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422
           ++GGTLFD VTP+MTIYKEEIFGPVL +VRV+ L EA+ LIN HEYGNG   +T DG  A
Sbjct: 371 YVGGTLFDNVTPDMTIYKEEIFGPVLSVVRVHDLAEAVDLINGHEYGNGVSCYTSDGGVA 430

Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWP 482
           R F  +I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +G+RFYT+ K+I QRWP
Sbjct: 431 RAFSRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYTRYKSIMQRWP 490

Query: 483 QRKSHEAAQFAFP 495
                + A+F  P
Sbjct: 491 D-SIGKGAEFTMP 502


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: 807
Number of extensions: 27
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: 505
Length adjustment: 34
Effective length of query: 464
Effective length of database: 471
Effective search space:   218544
Effective search space used:   218544
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 RR42_RS01580 RR42_RS01580 (methylmalonate-semialdehyde dehydrogenase)
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.15484.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-219  714.1   0.5   4.4e-219  713.9   0.5    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS01580  RR42_RS01580 methylmalonate-semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS01580  RR42_RS01580 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.9   0.5  4.4e-219  4.4e-219       2     477 .]      13     489 ..      12     489 .. 1.00

  Alignments for each domain:
  == domain 1  score: 713.9 bits;  conditional E-value: 4.4e-219
                                 TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                                h+i+G +  + sd++ +v npat+ v ++va  sa++vdaava+a+ +f+aw+et+ ++rar+l++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580  13 AHYIGGTVRAASSDRFADVFNPATGAVAGRVALGSAQDVDAAVAAAHAAFPAWSETAPLKRARILFKFK 81 
                                               69******************************************************************* PP

                                 TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGv 139
                                               +ll+ h+d++a li+ e+Gk+++dakG+v rG+e+ve+ac+++ ll+ + ++++   +d + +rqplGv
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580  82 ELLDRHHDDLAALITREHGKVFSDAKGEVTRGVEIVEFACGIPNLLKTDFTDNIGGGIDNWNLRQPLGV 150
                                               ********************************************************************* PP

                                 TIGR01722 140 vaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdr 208
                                               vaGitpfnfp m+p+wmfp+a+acGntfvlkpse++ps ++ +a+ll++aG+pdGv+nvv G+keavd 
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580 151 VAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSPSLLIADLLKQAGLPDGVFNVVQGGKEAVDA 219
                                               ********************************************************************* PP

                                 TIGR01722 209 llehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqr 277
                                               ll h dv+a+sfvGs++++eyiy+ g+++gkrvqal+Gaknh vv+pdad+++a+dal+gaa+G+aG+r
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580 220 LLAHKDVQALSFVGSTPIAEYIYTEGTRRGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGER 288
                                               ********************************************************************* PP

                                 TIGR01722 278 cmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlld 345
                                               cmais+av+vG++ ++lv+++ era+ +++  g +  ae+Gpl+t ++k++v+ +ia+g++eGa+++ d
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580 289 CMAISVAVAVGDVaDKLVPRLAERARSLKIRNGMQDDAEMGPLVTAAHKAKVEGYIAKGVEEGAKLVTD 357
                                               ************989****************************************************** PP

                                 TIGR01722 346 GrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsd 414
                                               Grg kv+G+e+G +vG tl+++v pdm+iykeeifGpvl v+++  l ea+ lin   yGnG + +tsd
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580 358 GRGHKVDGHENGFYVGGTLFDNVTPDMTIYKEEIFGPVLSVVRVHDLAEAVDLINGHEYGNGVSCYTSD 426
                                               ********************************************************************* PP

                                 TIGR01722 415 GaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               G+ ar f+ +i+vG+vG+nvpipvp++++sf+Gwk slfGd+h+yG++G+rfytr k +  rw
  lcl|FitnessBrowser__Cup4G11:RR42_RS01580 427 GGVARAFSRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYTRYKSIMQRW 489
                                               **************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (505 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: 7.43
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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SQLite3 databases

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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