Alignments for a candidate for mmsA in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Amycolatopsis halophila YIM 93223

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 WP_034271650.1 AMYHA_RS14120 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_000504245.1:WP_034271650.1
          Length = 507

 Score =  530 bits (1365), Expect = e-155
 Identities = 271/505 (53%), Positives = 344/505 (68%), Gaps = 10/505 (1%)

Query: 2   TLIKHLIGGELIADTG-RTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           T I H + G   A T    ADV NP+TG+   +V LA     Q  I +A  A  AW  T 
Sbjct: 3   TSIAHWVDGAEFAGTSDHWADVTNPATGQVSGRVALAGEHDAQHVIASAATAAKAWGETS 62

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
            AKR Q+LF F++LL + +E +  LI+ EHGK   DA GE+ RG E VE+A     +LKG
Sbjct: 63  LAKRTQILFAFRELLNSRKEELAHLITAEHGKVYSDALGEITRGQEVVEFACGISHLLKG 122

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
            YS +    +D  S   P+GVV  I+PFNFPAMVP+W +P+AIA GNT +LKPSE+DPS+
Sbjct: 123 GYSESASTGVDVHSKRDPLGVVGIISPFNFPAMVPMWFFPIAIASGNTVVLKPSEKDPSA 182

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
            L IA L+ EAGLP GV NV+ GDK AVDAL+ + +V A+SFVGSTPIA+Y+Y E ++ G
Sbjct: 183 ALWIANLWKEAGLPDGVFNVLQGDKVAVDALLHSQDVAAISFVGSTPIAKYVYEEASRHG 242

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNH V++PDADLD A  A + A YGS GERCMAISV V V D + D LV +
Sbjct: 243 KRVQALGGAKNHMVVLPDADLDLAADAAVNAGYGSAGERCMAISVLVAV-DPVGDDLVAR 301

Query: 301 LVPQIKGLKIGAG------TSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYK 354
           +  + + L  G G           DMGPLVT A RD+V G++ +G   GA+LV+DGR  +
Sbjct: 302 IAERTRTLVTGDGRKGDGPDGAEADMGPLVTKAHRDRVAGFVASGERAGAKLVIDGRTVE 361

Query: 355 VAGHENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCI 414
             G ++G +LG TLFD VTP+M IY EEIFGPVL +VR +S +EA++LIN +EYGNGT I
Sbjct: 362 ARGEQDGHWLGPTLFDHVTPDMDIYTEEIFGPVLAVVRASSYDEAVELINANEYGNGTAI 421

Query: 415 FTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKR 474
           FT DG AAR F  +++VGM+GVNVP+PVPVAY+SFGGWKRSLFGD HA+G +GV F+T+ 
Sbjct: 422 FTNDGGAARRFESDVQVGMIGVNVPIPVPVAYYSFGGWKRSLFGDTHAHGTEGVHFFTRA 481

Query: 475 KAITQRW--PQRKSHEAAQFAFPSN 497
           K +T RW  P  +     +  FP N
Sbjct: 482 KVVTTRWINPAARPEGGLELGFPQN 506


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: 736
Number of extensions: 25
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: 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 WP_034271650.1 AMYHA_RS14120 (CoA-acylating 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.2933700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-205  667.2   1.4   7.6e-205  667.0   1.4    1.0  1  NCBI__GCF_000504245.1:WP_034271650.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034271650.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.0   1.4  7.6e-205  7.6e-205       2     477 .]       6     488 ..       5     488 .. 0.98

  Alignments for each domain:
  == domain 1  score: 667.0 bits;  conditional E-value: 7.6e-205
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                            h++dG+   g+sd++ +v+npat++v ++va a  ++ +  +asa  +  aw+ets+a+r+++l+ +++ll+
  NCBI__GCF_000504245.1:WP_034271650.1   6 AHWVDGAEFAGTSDHWADVTNPATGQVSGRVALAGEHDAQHVIASAATAAKAWGETSLAKRTQILFAFRELLN 78 
                                           79*********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                            +++e+a+li+ae+Gk+++da G++ rG evve+ac+++ ll+G  +es ++ vdv+s r plGvv  i+pfn
  NCBI__GCF_000504245.1:WP_034271650.1  79 SRKEELAHLITAEHGKVYSDALGEITRGQEVVEFACGISHLLKGGYSESASTGVDVHSKRDPLGVVGIISPFN 151
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fpam+p+w fp+aia Gnt vlkpsek+psaa+ +a+l++eaG+pdGv+nv+ Gdk+avd ll+  dv a+sf
  NCBI__GCF_000504245.1:WP_034271650.1 152 FPAMVPMWFFPIAIASGNTVVLKPSEKDPSAALWIANLWKEAGLPDGVFNVLQGDKVAVDALLHSQDVAAISF 224
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292
                                           vGs+++++y+ye +s+hgkrvqal+Gaknhmvvlpdad++ a+da+v+a +G+aG+rcmais+ v+v  + ++
  NCBI__GCF_000504245.1:WP_034271650.1 225 VGSTPIAKYVYEEASRHGKRVQALGGAKNHMVVLPDADLDLAADAAVNAGYGSAGERCMAISVLVAVDPVgDD 297
                                           *********************************************************************99** PP

                             TIGR01722 293 lveeireraekvrvgag......ddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnf 359
                                           lv +i er + +  g g      d + a++Gpl+tk++++rva ++asg + Ga++++dGr+++  G ++G++
  NCBI__GCF_000504245.1:WP_034271650.1 298 LVARIAERTRTLVTGDGrkgdgpDGAEADMGPLVTKAHRDRVAGFVASGERAGAKLVIDGRTVEARGEQDGHW 370
                                           **********998776522222234679********************************************* PP

                             TIGR01722 360 vGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGv 432
                                           +G+tl+++v pdm iy eeifGpvl+v++a +++ea++lin++ yGnGtaift+dG+aar+f+ +++vG++Gv
  NCBI__GCF_000504245.1:WP_034271650.1 371 LGPTLFDHVTPDMDIYTEEIFGPVLAVVRASSYDEAVELINANEYGNGTAIFTNDGGAARRFESDVQVGMIGV 443
                                           ************************************************************************* PP

                             TIGR01722 433 nvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           nvpipvp++++sf+Gwk slfGd+h++G +Gv+f+tr+k+vt+rw
  NCBI__GCF_000504245.1:WP_034271650.1 444 NVPIPVPVAYYSFGGWKRSLFGDTHAHGTEGVHFFTRAKVVTTRW 488
                                           ********************************************* 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 34.34
//
[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 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