GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Stenotrophomonas chelatiphaga DSM 21508

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_001431535.1:WP_057507564.1
          Length = 501

 Score =  823 bits (2125), Expect = 0.0
 Identities = 400/496 (80%), Positives = 450/496 (90%)

Query: 8   PTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTP 67
           P ++LLIDG+FIES+T  W+DVVNPATQ+VLA+VPFAT  E+D AVA+ ++AFKTWRKTP
Sbjct: 6   PRIRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTP 65

Query: 68  IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127
           IG RARIFLKYQQLIRENM ELA  L+AEQGKT+ DAEGDVFRGLEVVEHAA IGNLQLG
Sbjct: 66  IGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLG 125

Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187
           ELANNVA GVDTYTL+QPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV
Sbjct: 126 ELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 185

Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAG 247
           TMRL ELALEAG+P GVLNVVHGG +VVNAICDHPDIKAVSFVGST+VGTHVYNRAS AG
Sbjct: 186 TMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLAG 245

Query: 248 KRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPDLV 307
           KRVQCMMGAKNHA+VLPDA+KEQTLN + GAAFGAAGQRCMA S +VLVGEA++W+PDLV
Sbjct: 246 KRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARSWVPDLV 305

Query: 308 AKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGN 367
           AKA+TLKV+AG  AGTDVGP++SC+A +RV GLI  G+ +GA L+LDGRNP V G+E GN
Sbjct: 306 AKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGN 365

Query: 368 FVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAA 427
           FVGPTIFSGVT +M +YQEEIFGPVL ++ A T+++AI L+N+NPNGNGTA+FT+SGAAA
Sbjct: 366 FVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAA 425

Query: 428 RHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTITERWF 487
           R FQE+IDVGQVGINVPIPVPVP+FSFTGSRASKLGDLGPYGKQVV FYTQTKTIT RWF
Sbjct: 426 RKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARWF 485

Query: 488 DENEVGGPVNTTINLK 503
           D+  +G  VNTTI+LK
Sbjct: 486 DDETLGHGVNTTISLK 501


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: 794
Number of extensions: 22
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: 503
Length of database: 501
Length adjustment: 34
Effective length of query: 469
Effective length of database: 467
Effective search space:   219023
Effective search space used:   219023
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_057507564.1 ABB28_RS04920 (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.559803.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-226  737.5   2.6   3.5e-226  737.3   2.6    1.0  1  NCBI__GCF_001431535.1:WP_057507564.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001431535.1:WP_057507564.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.3   2.6  3.5e-226  3.5e-226       1     477 []       8     484 ..       8     484 .. 1.00

  Alignments for each domain:
  == domain 1  score: 737.3 bits;  conditional E-value: 3.5e-226
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           +++lidG+f+e+ ++++ +v npat++vla+v++a++ evd ava+a+e+f +w++t++  rar++l+yq+l+
  NCBI__GCF_001431535.1:WP_057507564.1   8 IRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGTRARIFLKYQQLI 80 
                                           5899********************************************************************* PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           +e+  e+a+ +saeqGkt+ da+Gdv+rGlevveha ++  l lGe+ ++va+ vd+y++ qplGv+aGitpf
  NCBI__GCF_001431535.1:WP_057507564.1  81 RENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGELANNVANGVDTYTLMQPLGVCAGITPF 153
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpamiplwmfp+aia Gntfvlkpse++p  +++l el +eaG+p+GvlnvvhG++e v+ +++hpd+kavs
  NCBI__GCF_001431535.1:WP_057507564.1 154 NFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVS 226
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaake 292
                                           fvGs++vg ++y+++s  gkrvq+++Gaknh+vvlpda+ke++l+a+vgaa+GaaGqrcma s+ vlvG+a+ 
  NCBI__GCF_001431535.1:WP_057507564.1 227 FVGSTRVGTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARS 299
                                           ************************************************************************* PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           +v++++ +a+ ++v+ag+ +g+++Gp+i+ +a+erv+ liasg ++Ga + ldGr+ +v+G+e+GnfvG+t++
  NCBI__GCF_001431535.1:WP_057507564.1 300 WVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGNFVGPTIF 372
                                           ************************************************************************* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v +dm+iy+eeifGpvlv+lea+tle+ai+l+n +p GnGta+ft++Gaaarkfq +i+vGqvG+nvpipv
  NCBI__GCF_001431535.1:WP_057507564.1 373 SGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAARKFQEDIDVGQVGINVPIPV 445
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p+p+fsftG+++s  Gdl  yGkq v fyt++kt+tarw
  NCBI__GCF_001431535.1:WP_057507564.1 446 PVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARW 484
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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: 30.43
//
[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:

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:

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:

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:

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