Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate HSERO_RS15395 HSERO_RS15395 methylmalonate-semialdehyde dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS15395
          Length = 506

 Score =  690 bits (1781), Expect = 0.0
 Identities = 337/492 (68%), Positives = 399/492 (81%)

Query: 3   TSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKT 62
           + ++IP V L ++GE ++ST+++WRDV+NPATQEV+ARVPFAT EE+DRAVA+ ++ FKT
Sbjct: 2   SQANIPNVPLYLNGEKVQSTSKEWRDVLNPATQEVVARVPFATKEEVDRAVANAKETFKT 61

Query: 63  WRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIG 122
           WR T +  R RI LK+QQL+REN+  LA ++T E GKTL DAEG+V RGLEVVEHA  I 
Sbjct: 62  WRNTSLAQRMRIMLKFQQLLRENIAPLAELITREHGKTLPDAEGEVMRGLEVVEHACSIT 121

Query: 123 NLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE 182
           +LQLGELA NVA GVD YTL QPLGV AGIT FNFP M+P +MFP+A+A GNTFVLKPSE
Sbjct: 122 SLQLGELAENVAGGVDVYTLYQPLGVGAGITAFNFPVMLPCFMFPIAVACGNTFVLKPSE 181

Query: 183 QDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNR 242
           QDP  ++ L ELA +AG+PPGVLNVVHGGPDV N ICDHPDIKAVSF+GST VGTH+Y R
Sbjct: 182 QDPTSSLFLVELANQAGLPPGVLNVVHGGPDVANMICDHPDIKAVSFIGSTHVGTHIYRR 241

Query: 243 ASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAW 302
           AS+AGKR QCMMGAKNH IVLPDA K+Q +NNL GAAFGAAGQRCMA SVVVLVG+ + W
Sbjct: 242 ASEAGKRAQCMMGAKNHCIVLPDAPKDQAINNLLGAAFGAAGQRCMANSVVVLVGQTREW 301

Query: 303 IPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSG 362
           IP++V +++ +KV  G +   DVGPLVS AA +RV  LI  GV +GAKL LDGRN  V+G
Sbjct: 302 IPEIVERSKAMKVGPGTDRKADVGPLVSKAAKERVERLIASGVEQGAKLLLDGRNCKVAG 361

Query: 363 YENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTR 422
            ENGNFVGPT+F+GV  EM +Y +EIFGP +C++   T+DEAI  INANPNGNGT+IFT 
Sbjct: 362 SENGNFVGPTVFTGVKPEMDIYTQEIFGPAMCIVELDTLDEAIAFINANPNGNGTSIFTS 421

Query: 423 SGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTI 482
           SG AAR FQ EIDVGQVGINVPIPVPV  FSFTGSRASKLGDLGP GKQ V F+TQTKT+
Sbjct: 422 SGYAARKFQNEIDVGQVGINVPIPVPVAYFSFTGSRASKLGDLGPNGKQAVTFWTQTKTV 481

Query: 483 TERWFDENEVGG 494
           T RW+  +E  G
Sbjct: 482 TARWYAPDEEAG 493


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: 776
Number of extensions: 28
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: 506
Length adjustment: 34
Effective length of query: 469
Effective length of database: 472
Effective search space:   221368
Effective search space used:   221368
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 HSERO_RS15395 HSERO_RS15395 (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.29234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   4.7e-220  717.1   0.4   5.3e-220  717.0   0.4    1.0  1  FitnessBrowser__HerbieS:HSERO_RS15395  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS15395  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.0   0.4  5.3e-220  5.3e-220       2     477 .]      10     485 ..       9     485 .. 1.00

  Alignments for each domain:
  == domain 1  score: 717.0 bits;  conditional E-value: 5.3e-220
                              TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                             ++++G+ v+++s+++ +v npat+ev+a+v++a++eevd ava a+etf +w++ts+a+r r++l++q+ll
  FitnessBrowser__HerbieS:HSERO_RS15395  10 PLYLNGEKVQSTSKEWRDVLNPATQEVVARVPFATKEEVDRAVANAKETFKTWRNTSLAQRMRIMLKFQQLL 81 
                                            5799******************************************************************** PP

                              TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitp 145
                                            +e+   +a+li+ e+Gktl da+G+v+rGlevvehacs+tsl lGe+ e+va  vdvy++ qplGv aGit 
  FitnessBrowser__HerbieS:HSERO_RS15395  82 RENIAPLAELITREHGKTLPDAEGEVMRGLEVVEHACSITSLQLGELAENVAGGVDVYTLYQPLGVGAGITA 153
                                            ************************************************************************ PP

                              TIGR01722 146 fnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvka 217
                                            fnfp m+p +mfp+a+acGntfvlkpse++p++++ l el ++aG+p GvlnvvhG+ +  +++++hpd+ka
  FitnessBrowser__HerbieS:HSERO_RS15395 154 FNFPVMLPCFMFPIAVACGNTFVLKPSEQDPTSSLFLVELANQAGLPPGVLNVVHGGPDVANMICDHPDIKA 225
                                            ************************************************************************ PP

                              TIGR01722 218 vsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGa 289
                                            vsf+Gs++vg +iy+++s  gkr q+++Gaknh +vlpda k++a+++l+gaa+GaaGqrcma s++vlvG+
  FitnessBrowser__HerbieS:HSERO_RS15395 226 VSFIGSTHVGTHIYRRASEAGKRAQCMMGAKNHCIVLPDAPKDQAINNLLGAAFGAAGQRCMANSVVVLVGQ 297
                                            ************************************************************************ PP

                              TIGR01722 290 akelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvG 361
                                            ++e+++ei+er + ++vg+g+d  a++Gpl++k+akerv++liasg+++Ga++lldGr+ kv G e+GnfvG
  FitnessBrowser__HerbieS:HSERO_RS15395 298 TREWIPEIVERSKAMKVGPGTDRKADVGPLVSKAAKERVERLIASGVEQGAKLLLDGRNCKVAGSENGNFVG 369
                                            ************************************************************************ PP

                              TIGR01722 362 itllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvn 433
                                            +t++++vkp+m iy +eifGp ++++e dtl+eai++in++p GnGt+ifts+G aarkfq ei+vGqvG+n
  FitnessBrowser__HerbieS:HSERO_RS15395 370 PTVFTGVKPEMDIYTQEIFGPAMCIVELDTLDEAIAFINANPNGNGTSIFTSSGYAARKFQNEIDVGQVGIN 441
                                            ************************************************************************ PP

                              TIGR01722 434 vpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                            vpipvp+++fsftG+++s  Gdl   Gkq v f+t++ktvtarw
  FitnessBrowser__HerbieS:HSERO_RS15395 442 VPIPVPVAYFSFTGSRASKLGDLGPNGKQAVTFWTQTKTVTARW 485
                                            ******************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (506 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: 33.59
//
[ok]

This GapMind analysis is from Apr 09 2024. 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