Alignments for a candidate for mmsA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Halomonas desiderata SP1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_086508312.1 BZY95_RS01885 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::psRCH2:GFF2388
         (503 letters)



>NCBI__GCF_002151265.1:WP_086508312.1
          Length = 499

 Score =  684 bits (1764), Expect = 0.0
 Identities = 338/497 (68%), Positives = 398/497 (80%)

Query: 6   SIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRK 65
           SI  + + IDG+ + S +Q+WRDV+NPATQEV+ARVPF TAEE+DRAVAS ++AFKTWRK
Sbjct: 2   SIREIPMYIDGQAVPSQSQEWRDVINPATQEVVARVPFCTAEEVDRAVASAKEAFKTWRK 61

Query: 66  TPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQ 125
           TP+  R RI L  Q LIRE+ +ELAA++T E GKTL DA G+V RGLEVVEHA  I +LQ
Sbjct: 62  TPLAKRMRIMLTLQALIREHTEELAALITEEHGKTLPDAAGEVGRGLEVVEHACSITSLQ 121

Query: 126 LGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDP 185
           LGELA N A  VD YTL QPLGV AGIT FNFP M+P +MFP+AIATGNTFVLKPSEQDP
Sbjct: 122 LGELAENAANEVDVYTLNQPLGVGAGITAFNFPIMLPCFMFPLAIATGNTFVLKPSEQDP 181

Query: 186 MVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQ 245
             TMRL ELA EAGVP GVLNVVHGGPDV N ICDHPDIKA+SF+GST VGTH+Y RAS+
Sbjct: 182 SSTMRLVELAHEAGVPAGVLNVVHGGPDVANQICDHPDIKALSFIGSTNVGTHIYRRASE 241

Query: 246 AGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPD 305
           AGKRVQ MMGAKNH +V+PDA++ Q +NNL G+AFGAAGQRCMA SVVVLVGEA  W+ D
Sbjct: 242 AGKRVQSMMGAKNHCVVMPDANRSQAINNLLGSAFGAAGQRCMANSVVVLVGEANQWLDD 301

Query: 306 LVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYEN 365
           +V  A+ +KV  G +   D+GPLVS AA DRV  LI+ G +EGA+L +DGR   V GY +
Sbjct: 302 IVEGARNMKVGPGTQRDADLGPLVSKAARDRVVRLIDAGEKEGARLLVDGRGYQVEGYPD 361

Query: 366 GNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGA 425
           GNFVG T+F+ V  EM++Y+EEIFGPVLCV++  T+DEAI  INANPNGNGT+IFT SG 
Sbjct: 362 GNFVGATVFADVKPEMTIYREEIFGPVLCVVSVDTLDEAIAFINANPNGNGTSIFTNSGW 421

Query: 426 AARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTITER 485
            AR F+ +IDVGQVGINVPIPVPV  FSFTGSR SKLGDLGP GKQ +QF+TQTKT+T R
Sbjct: 422 VARRFETDIDVGQVGINVPIPVPVAYFSFTGSRGSKLGDLGPNGKQAIQFWTQTKTVTAR 481

Query: 486 WFDENEVGGPVNTTINL 502
           WF+   V   +N+TI+L
Sbjct: 482 WFEPENVSSGINSTISL 498


Lambda     K      H
   0.318    0.134    0.394 

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: 743
Number of extensions: 32
Number of successful extensions: 1
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: 503
Length of database: 499
Length adjustment: 34
Effective length of query: 469
Effective length of database: 465
Effective search space:   218085
Effective search space used:   218085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_086508312.1 BZY95_RS01885 (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.11774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-223  726.1   0.6     1e-222  725.9   0.6    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508312.1  BZY95_RS01885 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508312.1  BZY95_RS01885 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.9   0.6    1e-222    1e-222       3     477 .]       8     482 ..       6     482 .. 1.00

  Alignments for each domain:
  == domain 1  score: 725.9 bits;  conditional E-value: 1e-222
                                 TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqa 71 
                                               ++idG+ v ++s+++ +v npat+ev+a+v++++aeevd avasa+e+f +w++t++a+r r++l  qa
  lcl|NCBI__GCF_002151265.1:WP_086508312.1   8 MYIDGQAVPSQSQEWRDVINPATQEVVARVPFCTAEEVDRAVASAKEAFKTWRKTPLAKRMRIMLTLQA 76 
                                               69******************************************************************* PP

                                 TIGR01722  72 llkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvv 140
                                               l++eh +e+a li+ e+Gktl da G+v rGlevvehacs+tsl lGe+ e+ a++vdvy+++qplGv 
  lcl|NCBI__GCF_002151265.1:WP_086508312.1  77 LIREHTEELAALITEEHGKTLPDAAGEVGRGLEVVEHACSITSLQLGELAENAANEVDVYTLNQPLGVG 145
                                               ********************************************************************* PP

                                 TIGR01722 141 aGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrl 209
                                               aGit fnfp m+p +mfplaia Gntfvlkpse++ps++++l el +eaG+p GvlnvvhG+ +  +++
  lcl|NCBI__GCF_002151265.1:WP_086508312.1 146 AGITAFNFPIMLPCFMFPLAIATGNTFVLKPSEQDPSSTMRLVELAHEAGVPAGVLNVVHGGPDVANQI 214
                                               ********************************************************************* PP

                                 TIGR01722 210 lehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrc 278
                                               ++hpd+ka+sf+Gs++vg +iy+++s  gkrvq+++Gaknh vv+pda++ +a+++l+g+a+GaaGqrc
  lcl|NCBI__GCF_002151265.1:WP_086508312.1 215 CDHPDIKALSFIGSTNVGTHIYRRASEAGKRVQSMMGAKNHCVVMPDANRSQAINNLLGSAFGAAGQRC 283
                                               ********************************************************************* PP

                                 TIGR01722 279 maisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGr 347
                                               ma s++vlvG+a++++++i+e a+ ++vg+g++  a+lGpl++k+a++rv +li++g keGa++l+dGr
  lcl|NCBI__GCF_002151265.1:WP_086508312.1 284 MANSVVVLVGEANQWLDDIVEGARNMKVGPGTQRDADLGPLVSKAARDRVVRLIDAGEKEGARLLVDGR 352
                                               ********************************************************************* PP

                                 TIGR01722 348 gykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGa 416
                                               gy+veGy++GnfvG t++++vkp+m+iy+eeifGpvl+v+ +dtl+eai++in++p GnGt+ift++G 
  lcl|NCBI__GCF_002151265.1:WP_086508312.1 353 GYQVEGYPDGNFVGATVFADVKPEMTIYREEIFGPVLCVVSVDTLDEAIAFINANPNGNGTSIFTNSGW 421
                                               ********************************************************************* PP

                                 TIGR01722 417 aarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                ar+f+ +i+vGqvG+nvpipvp+++fsftG+++s  Gdl   Gkq ++f+t++ktvtarw
  lcl|NCBI__GCF_002151265.1:WP_086508312.1 422 VARRFETDIDVGQVGINVPIPVPVAYFSFTGSRGSKLGDLGPNGKQAIQFWTQTKTVTARW 482
                                               ************************************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (499 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: 12.77
//
[ok]

This GapMind analysis is from Sep 24 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