Alignments for a candidate for mmsA in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pandoraea thiooxydans ATSB16

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_047216758.1 PATSB16_RS19035 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_001931675.1:WP_047216758.1
          Length = 502

 Score =  640 bits (1651), Expect = 0.0
 Identities = 312/494 (63%), Positives = 386/494 (78%), Gaps = 3/494 (0%)

Query: 3   LIKHLIGGELIA-DTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61
           +I H IGG+L A  +GR ADVFNP+ G    +V LA    +  A+ AA+AA+PAW  T P
Sbjct: 8   VINHYIGGQLRAGQSGREADVFNPAEGAVSARVALASEAEVDAAVAAARAAWPAWAATAP 67

Query: 62  AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121
            KRA++LF FK LLE + + + +LI+ EHGK   DA GE+ RGIE VE+A  AP +L G+
Sbjct: 68  LKRARILFNFKALLEQHHDELARLITSEHGKVFSDAKGEVTRGIEVVEFACGAPHLLNGQ 127

Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181
           +S N+G  ID WS  QPIGV AGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS++
Sbjct: 128 HSDNIGGGIDNWSLRQPIGVCAGITPFNFPVMVPMWMFPIALACGNTFVLKPSERDPSAS 187

Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241
           LL+A+L  +AGLP GV NVV GDK AVDAL+  P+V+A+SFVGSTPIA+YIYSEGT+RGK
Sbjct: 188 LLMADLLRQAGLPDGVFNVVQGDKVAVDALLAHPDVEAVSFVGSTPIAQYIYSEGTRRGK 247

Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301
           RVQALGGAKNH V+MPDADLD AV ALMGAAYGS GERCMAISVAV VG  +ADALV++L
Sbjct: 248 RVQALGGAKNHLVVMPDADLDQAVDALMGAAYGSAGERCMAISVAVAVG-HVADALVERL 306

Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361
           VP++K L +  GT    +MGPLVTGA + KV GYI  GV +GA+L+VDGRG +VAGHE G
Sbjct: 307 VPRVKALCVAPGTDARAEMGPLVTGAHKAKVEGYIAKGVEEGAKLLVDGRGLRVAGHEQG 366

Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421
           FF+GGTLFD V  +MTIY+EEIFGPVLC+VRV     A++LIN HE+GNG   +T DG  
Sbjct: 367 FFVGGTLFDDVRTDMTIYREEIFGPVLCVVRVPDFAAAVELINAHEFGNGVSCYTSDGGV 426

Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481
           AR F  +I++GMVG+NVP+PVP+A+HSFGGWK+SLFGD HAYG +GVRFYT+ K++ QRW
Sbjct: 427 ARTFARQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSVMQRW 486

Query: 482 PQRKSHEAAQFAFP 495
           P   + + A+F  P
Sbjct: 487 PDSIA-KGAEFTMP 499


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: 784
Number of extensions: 30
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: 502
Length adjustment: 34
Effective length of query: 464
Effective length of database: 468
Effective search space:   217152
Effective search space used:   217152
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_047216758.1 PATSB16_RS19035 (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.3711097.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-222  724.0   0.8   4.4e-222  723.8   0.8    1.0  1  NCBI__GCF_001931675.1:WP_047216758.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001931675.1:WP_047216758.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.8   0.8  4.4e-222  4.4e-222       1     477 []       9     486 ..       9     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 723.8 bits;  conditional E-value: 4.4e-222
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           ++h+i+G++  g+s++  +v npa++ v a+va as +evdaava+ar +++awa t+ ++rar+l+ ++all
  NCBI__GCF_001931675.1:WP_047216758.1   9 INHYIGGQLRAGQSGREADVFNPAEGAVSARVALASEAEVDAAVAAARAAWPAWAATAPLKRARILFNFKALL 81 
                                           68*********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           ++h+de+a+li++e+Gk+++dakG+v rG+evve+ac+ + ll G+ ++++   +d +s+rqp+Gv+aGitpf
  NCBI__GCF_001931675.1:WP_047216758.1  82 EQHHDELARLITSEHGKVFSDAKGEVTRGIEVVEFACGAPHLLNGQHSDNIGGGIDNWSLRQPIGVCAGITPF 154
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfp m+p+wmfp+a+acGntfvlkpse++psa++ +a+ll++aG+pdGv+nvv Gdk+avd ll hpdv avs
  NCBI__GCF_001931675.1:WP_047216758.1 155 NFPVMVPMWMFPIALACGNTFVLKPSERDPSASLLMADLLRQAGLPDGVFNVVQGDKVAVDALLAHPDVEAVS 227
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.k 291
                                           fvGs+++++yiy+ g+++gkrvqal+Gaknh vv+pdad+++a+dal+gaa+G+aG+rcmais+av+vG + +
  NCBI__GCF_001931675.1:WP_047216758.1 228 FVGSTPIAQYIYSEGTRRGKRVQALGGAKNHLVVMPDADLDQAVDALMGAAYGSAGERCMAISVAVAVGHVaD 300
                                           **********************************************************************989 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                            lve+++ r++ + v++g+d+ ae+Gpl+t ++k++v+ +ia+g++eGa++l+dGrg++v G+e+G fvG tl
  NCBI__GCF_001931675.1:WP_047216758.1 301 ALVERLVPRVKALCVAPGTDARAEMGPLVTGAHKAKVEGYIAKGVEEGAKLLVDGRGLRVAGHEQGFFVGGTL 373
                                           9************************************************************************ PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           +++v++dm+iy+eeifGpvl+v+++  +  a++lin+  +GnG + +tsdG+ ar+f  +i++G+vG+nvpip
  NCBI__GCF_001931675.1:WP_047216758.1 374 FDDVRTDMTIYREEIFGPVLCVVRVPDFAAAVELINAHEFGNGVSCYTSDGGVARTFARQIQIGMVGINVPIP 446
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           vp++++sf+Gwk+slfGd+h+yG++Gvrfytr k v  rw
  NCBI__GCF_001931675.1:WP_047216758.1 447 VPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSVMQRW 486
                                           ***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (502 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: 22.95
//
[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