Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate GFF927 HP15_906 methylmalonate-semialdehyde dehydrogenase

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__Marino:GFF927
          Length = 497

 Score =  728 bits (1879), Expect = 0.0
 Identities = 358/490 (73%), Positives = 407/490 (83%), Gaps = 1/490 (0%)

Query: 9   IAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKETPVSERAR 68
           IAG F++      I V+NP  N  +A+    +  ++EQA+  A E F +WKE PVSERAR
Sbjct: 8   IAGEFIQSQTKDWIEVTNPATNEVIAKAPNTTHAEMEQAIKYAGEVFKTWKEVPVSERAR 67

Query: 69  VMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLLMGETVENV 128
           VMLRYQALLK+HHDE+A+I+S E GKTFEDAKGDVWRGIEVVEHA NV SL+MGETVENV
Sbjct: 68  VMLRYQALLKKHHDEIAEILSQETGKTFEDAKGDVWRGIEVVEHAGNVASLMMGETVENV 127

Query: 129 ARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVPLTSVRLAE 188
           AR +DT+S  QPLGVC GITPFNFPAMIPLWMFP+AIACGN FILKPSEQ PLT +RLAE
Sbjct: 128 AREVDTHSWIQPLGVCAGITPFNFPAMIPLWMFPMAIACGNTFILKPSEQDPLTPMRLAE 187

Query: 189 LFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTAHNKRVQSF 248
           LF EAGAPKGVLQVVHGGKEQVD LL  P +KAVSFVGSV VG+Y+Y TGT + KRVQSF
Sbjct: 188 LFEEAGAPKGVLQVVHGGKEQVDVLLTDPAIKAVSFVGSVPVGRYIYETGTRNMKRVQSF 247

Query: 249 AGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPEIRDALAKV 308
           AGAKNHMVI+PDADK QVI+ LVGASVGAAGQRCMAISVAV VG A++WIPE+++A+AKV
Sbjct: 248 AGAKNHMVILPDADKQQVINALVGASVGAAGQRCMAISVAVFVGEAQQWIPELKEAMAKV 307

Query: 309 RPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPDGNWVGPTL 368
           RPG W+DSGASYGP+I+ +AK RIE LI  G  +GA LLLDGRG  V+G PDGNWVGPTL
Sbjct: 308 RPGAWNDSGASYGPIISAKAKDRIESLIATGEAQGANLLLDGRGCTVDGLPDGNWVGPTL 367

Query: 369 FAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGAAARTFQHH 428
           F+GV  +M IY EE+FGPVL   E D+L  AI L+N SPYGNG SIFTSSG AAR FQH 
Sbjct: 368 FSGVTTEMDIYNEEIFGPVLSCMETDTLGDAIELVNNSPYGNGVSIFTSSGGAARRFQHE 427

Query: 429 IEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTARWFDSDSVA 488
           I+VGQVG+NIPIPVPLPFFSFTGWKGSFYGD HAYGKQ VRFYTETKTVT+RWF S++ +
Sbjct: 428 IDVGQVGVNIPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTVTSRWFSSEATS 487

Query: 489 G-TNFSIQMR 497
              NFSIQ+R
Sbjct: 488 SEANFSIQLR 497


Lambda     K      H
   0.319    0.135    0.406 

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: 870
Number of extensions: 26
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate GFF927 HP15_906 (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.21366.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-251  820.4   0.5   2.6e-251  820.2   0.5    1.0  1  lcl|FitnessBrowser__Marino:GFF927  HP15_906 methylmalonate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF927  HP15_906 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.2   0.5  2.6e-251  2.6e-251       2     477 .]       5     480 ..       4     480 .. 1.00

  Alignments for each domain:
  == domain 1  score: 820.2 bits;  conditional E-value: 2.6e-251
                          TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehr 77 
                                         ++i+G+f++++++ +i+v+npatnev+ak + ++ +e+++a+  a e f +w+e +v+erarv+lryqallk+h+
  lcl|FitnessBrowser__Marino:GFF927   5 PLYIAGEFIQSQTKDWIEVTNPATNEVIAKAPNTTHAEMEQAIKYAGEVFKTWKEVPVSERARVMLRYQALLKKHH 80 
                                        689************************************************************************* PP

                          TIGR01722  78 deiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamip 153
                                        deia+++s e Gkt+edakGdv+rG+evveha +v+sl++Getve+va++vd++s  qplGv+aGitpfnfpamip
  lcl|FitnessBrowser__Marino:GFF927  81 DEIAEILSQETGKTFEDAKGDVWRGIEVVEHAGNVASLMMGETVENVAREVDTHSWIQPLGVCAGITPFNFPAMIP 156
                                        **************************************************************************** PP

                          TIGR01722 154 lwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgey 229
                                        lwmfp+aiacGntf+lkpse++p++ ++lael++eaGap+Gvl+vvhG+ke+vd ll  p +kavsfvGsv+vg+y
  lcl|FitnessBrowser__Marino:GFF927 157 LWMFPMAIACGNTFILKPSEQDPLTPMRLAELFEEAGAPKGVLQVVHGGKEQVDVLLTDPAIKAVSFVGSVPVGRY 232
                                        **************************************************************************** PP

                          TIGR01722 230 iyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvr 305
                                        iyetg+++ krvq++aGaknhmv+lpdadk+++++alvga+vGaaGqrcmais+av vG+a+++++e++e+++kvr
  lcl|FitnessBrowser__Marino:GFF927 233 IYETGTRNMKRVQSFAGAKNHMVILPDADKQQVINALVGASVGAAGQRCMAISVAVFVGEAQQWIPELKEAMAKVR 308
                                        **************************************************************************** PP

                          TIGR01722 306 vgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifG 381
                                        +ga++d+ga++Gp+i+ +ak+r++slia+g ++Ga++lldGrg +v+G ++Gn+vG+tl+++v ++m iy+eeifG
  lcl|FitnessBrowser__Marino:GFF927 309 PGAWNDSGASYGPIISAKAKDRIESLIATGEAQGANLLLDGRGCTVDGLPDGNWVGPTLFSGVTTEMDIYNEEIFG 384
                                        **************************************************************************** PP

                          TIGR01722 382 pvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlh 457
                                        pvl  +e+dtl +ai+l+n+spyGnG +ifts+G+aar+fqhei+vGqvGvn+pipvplpffsftGwk+s++Gd+h
  lcl|FitnessBrowser__Marino:GFF927 385 PVLSCMETDTLGDAIELVNNSPYGNGVSIFTSSGGAARRFQHEIDVGQVGVNIPIPVPLPFFSFTGWKGSFYGDQH 460
                                        **************************************************************************** PP

                          TIGR01722 458 iyGkqGvrfytrlktvtarw 477
                                        +yGkq vrfyt++ktvt+rw
  lcl|FitnessBrowser__Marino:GFF927 461 AYGKQAVRFYTETKTVTSRW 480
                                        ******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (497 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: 00:00:00.02
# Mc/sec: 9.56
//
[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