GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Bacillus altitudinis 41KF2b

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000691145.1:WP_019744147.1
          Length = 486

 Score =  675 bits (1741), Expect = 0.0
 Identities = 322/481 (66%), Positives = 403/481 (83%), Gaps = 2/481 (0%)

Query: 3   EIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSK 62
           +++ LKNYI G+WV+++T+Q E V NPAT EV+ +VP+STK D+++A Q A EAF TWSK
Sbjct: 5   DVQTLKNYIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSK 64

Query: 63  VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122
            AVPRRARILF +QQLL +  +ELA L+T+ENGK+  EA GEV RGIE VEFAAGAP+LM
Sbjct: 65  TAVPRRARILFKYQQLLVEKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLM 124

Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182
           MG  L  IAT +E+  YRYPIGV+GGI PFNFPMMVPCWMFP+AIA GNTF+LKPSERTP
Sbjct: 125 MGKQLPDIATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTP 184

Query: 183 LLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSE 242
           +L  +L ELFE+AGLPKGV N+V GAHDVVNG+LEH ++KAISFVGS+PV EYVYKKG+ 
Sbjct: 185 ILAARLAELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTA 244

Query: 243 NLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302
           + KRVQ+L GAKNH+IVL DA+LE     I+GAAFGSAGERCMA AVV VEE +AD+ + 
Sbjct: 245 HGKRVQALAGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDVADDLIQ 304

Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN--VSDD 360
           +L ++   + IGNG++  VFLGPVIR+++K+RTL YI+ G+EEGA L+ DGR++   + +
Sbjct: 305 QLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQDNETNGE 364

Query: 361 GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSN 420
           GYFVGPTIFD+VT +M IW+DEIFAPVLS++RV +L EAI+++N+S+FANGACL+T +++
Sbjct: 365 GYFVGPTIFDHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSAS 424

Query: 421 AIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480
           +IR FRENI+AGMLGIN+GVPAPMAFFPFSGWK SF+G LHANG D V+FYTRKK+VTAR
Sbjct: 425 SIREFRENIEAGMLGINIGVPAPMAFFPFSGWKDSFYGDLHANGTDGVEFYTRKKMVTAR 484

Query: 481 Y 481
           Y
Sbjct: 485 Y 485


Lambda     K      H
   0.318    0.136    0.396 

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: 707
Number of extensions: 23
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: 487
Length of database: 486
Length adjustment: 34
Effective length of query: 453
Effective length of database: 452
Effective search space:   204756
Effective search space used:   204756
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_019744147.1 BA79_RS03900 (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.1263542.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-185  602.4   0.4   3.3e-185  602.2   0.4    1.0  1  NCBI__GCF_000691145.1:WP_019744147.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_019744147.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.2   0.4  3.3e-185  3.3e-185       2     477 .]      10     485 ..       9     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 602.2 bits;  conditional E-value: 3.3e-185
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                           k +i+G+ v++++++   v npat+ev+a+v+ +++ +v+ av +a+e+f++w++t+v +rar+l++yq+ll 
  NCBI__GCF_000691145.1:WP_019744147.1  10 KNYIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRARILFKYQQLLV 82 
                                           789********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                           e+ de+a+l+++e+Gk +++akG+v rG+e ve+a + ++l++G+  +++a+ ++   +r p+Gv+ Gitpfn
  NCBI__GCF_000691145.1:WP_019744147.1  83 EKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPDIATGLESGMYRYPIGVIGGITPFN 155
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fp m+p wmfplaiacGntfvlkpse+ p  a +lael++eaG+p+Gvln+v G ++ v+ lleh +vka+sf
  NCBI__GCF_000691145.1:WP_019744147.1 156 FPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLAELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISF 228
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292
                                           vGs++v+ey+y++g+ahgkrvqalaGaknh +vl dad+e+a ++++gaa+G+aG+rcma +++ +  ++ ++
  NCBI__GCF_000691145.1:WP_019744147.1 229 VGSQPVAEYVYKKGTAHGKRVQALAGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDVaDD 301
                                           ************************************************************87655555545** PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           l++++++  +++ +g g +    lGp+i k++ker  ++i+sg++eGa+++ dGr    e   eG fvG+t++
  NCBI__GCF_000691145.1:WP_019744147.1 302 LIQQLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQD-NETNGEGYFVGPTIF 373
                                           *******************************************************75.578889********* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v  +mki+++eif pvl ++++ +l eai l n+s + nG++++t + ++ r+f+ +ie+G++G+n+ +p 
  NCBI__GCF_000691145.1:WP_019744147.1 374 DHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSASSIREFRENIEAGMLGINIGVPA 446
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p++ff f+Gwkds++Gdlh+ G +Gv+fytr k+vtar+
  NCBI__GCF_000691145.1:WP_019744147.1 447 PMAFFPFSGWKDSFYGDLHANGTDGVEFYTRKKMVTARY 485
                                           *************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (486 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: 30.72
//
[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:

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