Alignments for a candidate for putA in Methylocapsa acidiphila B2

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Methylocapsa acidiphila B2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_026607825.1 METAC_RS0116005 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_000427445.1:WP_026607825.1
          Length = 1032

 Score =  877 bits (2267), Expect = 0.0
 Identities = 477/1026 (46%), Positives = 656/1026 (63%), Gaps = 12/1026 (1%)

Query: 33   YIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQQYSLET 92
            Y   +E   + L+     SD A  R+   A  L+   R+  +K  + G++  L++YSL +
Sbjct: 14   YAPADESVAAALLAQADLSDAAEARIDSLATRLIKAARE--QKFRIGGVEDLLREYSLSS 71

Query: 93   QEGIILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGLMLTGKI 152
            +EG+ LM LAEALLR+PD  TAD LIED+L+ A W  H   S+++LV+A+ W L  T K+
Sbjct: 72   EEGLALMTLAEALLRVPDDFTADLLIEDRLASAHWASHADGSEALLVSAAAWALGTTAKV 131

Query: 153  VKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKNSEDKRK 212
            ++  K   G    +++ L  R+G   +R A   A+++MG  FV G T+++ L+ +  +  
Sbjct: 132  MEKGKSAHG----VVAALGRRIGMGALRAAARQAVQLMGAHFVFGETIEQTLRQAASREG 187

Query: 213  LGYTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTISIKLSALHPRY 272
              +  S+DMLGE A T+ DA+ YF+ YA+AI  +GAQ+  +    R  IS+KLSALHPRY
Sbjct: 188  RNWRFSFDMLGEGARTQVDADSYFSAYAHAIEAIGAQAAGDAAPGRLGISVKLSALHPRY 247

Query: 273  EVANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWG 332
            E  +  RVL EL   V  L + AR   +  +IDAEE DRLELSL +   L    +  GW 
Sbjct: 248  EPQSRGRVLAELTPRVAELARAARRHGLIFTIDAEEADRLELSLDIVDLLLADRSLAGWH 307

Query: 333  LLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYT 392
              G+ VQAY KRA   +  +   A+     + +RLVKGAYWDSE+K AQ+ G A YP++T
Sbjct: 308  GFGLAVQAYQKRAAAAIDHVVATARLCDRRLTLRLVKGAYWDSEIKRAQERGLADYPVFT 367

Query: 393  RKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQRLHGMGQE 452
            RKA TD++YLACAR LL  A R  I+PQFA+HNA TVA+I +MAGD   EFQRLHGMG+E
Sbjct: 368  RKAMTDLNYLACARRLL--AARDVIFPQFATHNALTVASIVEMAGDAGFEFQRLHGMGEE 425

Query: 453  LYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVVH 512
            L++ +  E    + R+YAP+GAH +LL YLVRRLLENGAN+SFV +L DP     +L+V 
Sbjct: 426  LFEALRIERPTLSSRVYAPVGAHANLLAYLVRRLLENGANSSFVARLGDPHVAPRALLVR 485

Query: 513  PLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAGP 572
            P   +         ++ LP D+ G  RK ++G+        +    A+ K  +   +A P
Sbjct: 486  PQAVIGDASRARTARLPLPQDLHGPARKTAQGIEFGDRRAVDALTQAIGKAAALA-EAAP 544

Query: 573  LVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRASA 632
            +V+G+   G  +++ SP D   T+G V       + +A+  A A F  W++TPVE RAS 
Sbjct: 545  IVSGRRREGVLRSLASPIDGA-TIGVVGETPVRILTEAMREARAGFRLWSQTPVEARASC 603

Query: 633  LQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLPG 692
            L+++A  LE    + + L   EAGK++ D + E REA+DFCRYYA +A++L +   +LPG
Sbjct: 604  LERVAQDLEGQAPKWLRLLQIEAGKTLDDAVGEWREAIDFCRYYAQEARRLFAASVVLPG 663

Query: 693  PTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQ 752
            PTGE N L  + RGVF CISPWNFPL+IF GQV+AALAAGN+V+AKPAEQT +I    V 
Sbjct: 664  PTGEDNRLSWRSRGVFACISPWNFPLSIFTGQVAAALAAGNSVLAKPAEQTPLIAAAIVA 723

Query: 753  LAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAIIP 812
              H+AG P + L  LPG G  +G  L A   + GV FTGS  TA  INR LA ++GAI  
Sbjct: 724  AFHRAGAPVEALHLLPGDG-EIGAGLVALPALAGVAFTGSMETAVRINRALAAKDGAIAT 782

Query: 813  LIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQG 872
            LIAETGG N M+ D+T+ PEQV +DV++SSF SAGQRCSALR+L +QED AD++I ++ G
Sbjct: 783  LIAETGGVNVMIADATALPEQVADDVLASSFRSAGQRCSALRLLCIQEDAADKIIAMIAG 842

Query: 873  AMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMSLP-AGTENGHFVS 931
            A  EL++G+P  +   VGPVID  AK +L+AHI  +++   +     +P +   NG +V+
Sbjct: 843  AARELLVGDPRDLSVHVGPVIDLAAKTSLEAHIAAMRRRAIVRYAGEIPTSAPRNGFYVA 902

Query: 932  PTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHALEV 991
            P   E+     L++E FGPILHV+RYKA+EL  ++D++ + G+GLTLG+HSR +     +
Sbjct: 903  PHIFELAQPTDLDREVFGPILHVVRYKANELDRLLDQLEAMGYGLTLGVHSRIDATIAHI 962

Query: 992  ADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIG 1051
             ++   GN Y+NRN IGAVVG QPFGG GLSGTGPKAGGPHYL RF  E+T T N  A+G
Sbjct: 963  MERRLAGNCYVNRNMIGAVVGTQPFGGFGLSGTGPKAGGPHYLERFCVEQTVTINTAAVG 1022

Query: 1052 GNATLL 1057
            GNA L+
Sbjct: 1023 GNAALV 1028


Lambda     K      H
   0.317    0.133    0.377 

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: 2328
Number of extensions: 111
Number of successful extensions: 7
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: 1064
Length of database: 1032
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 987
Effective search space:  1005753
Effective search space used:  1005753
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_026607825.1 METAC_RS0116005 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01238.hmm
# target sequence database:        /tmp/gapView.48433.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.4e-181  588.7   0.4   7.6e-181  587.9   0.4    1.4  1  NCBI__GCF_000427445.1:WP_026607825.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000427445.1:WP_026607825.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.9   0.4  7.6e-181  7.6e-181       1     496 [.     506    1009 ..     506    1013 .. 0.97

  Alignments for each domain:
  == domain 1  score: 587.9 bits;  conditional E-value: 7.6e-181
                             TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                            dl+g +rk ++G+++   + ++ l + + kaaa   +aapiv+   + eg  + + +p d    +G v e+
  NCBI__GCF_000427445.1:WP_026607825.1  506 DLHGPARKTAQGIEFGDRRAVDALTQAIGKAAAL-AEAAPIVS-GRRREGVLRSLASPIDGA-TIGVVGET 573 
                                            78999**********************9998775.69*****5.567799*********975.68****** PP

                             TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 
                                                  ea+  a a f  ws t+ + ra++ler+a+ le + p+ + ll+ eaGktl++a+ e rea+df+
  NCBI__GCF_000427445.1:WP_026607825.1  574 PVRILTEAMREARAGFRLWSQTPVEARASCLERVAQDLEGQAPKWLRLLQIEAGKTLDDAVGEWREAIDFC 644 
                                            *********************************************************************** PP

                             TIGR01238  143 ryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqts 200 
                                            ryya++++  +    + +             +G++ cispwnfpl+iftGq+aaalaaGn+v+akpaeqt+
  NCBI__GCF_000427445.1:WP_026607825.1  645 RYYAQEARRLFAASVVLPgptgednrlswrsRGVFACISPWNFPLSIFTGQVAAALAAGNSVLAKPAEQTP 715 
                                            **********99998888999************************************************** PP

                             TIGR01238  201 liaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvplia 271 
                                            liaa  v+ ++ aG p  ++ llpG Ge +Ga l + +++aGv+ftGs e+a +in+ala ++ a ++lia
  NCBI__GCF_000427445.1:WP_026607825.1  716 LIAAAIVAAFHRAGAPVEALHLLPGDGE-IGAGLVALPALAGVAFTGSMETAVRINRALAAKDGAIATLIA 785 
                                            ****************************.****************************************** PP

                             TIGR01238  272 etGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlt 342 
                                            etGG n mi d+tal+eqv  dvlas+f saGqrcsalr+lc+qed ad+++ +i Ga  el vg p  l 
  NCBI__GCF_000427445.1:WP_026607825.1  786 ETGGVNVMIADATALPEQVADDVLASSFRSAGQRCSALRLLCIQEDAADKIIAMIAGAARELLVGDPRDLS 856 
                                            *********************************************************************** PP

                             TIGR01238  343 tdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvv 413 
                                              vGpvid  ak  l+ahi +m+ +a   +        + ++g +vap +fel +  +l++evfGp+lhvv
  NCBI__GCF_000427445.1:WP_026607825.1  857 VHVGPVIDLAAKTSLEAHIAAMRRRAIVRYAGEIPT-SAPRNGFYVAPHIFELAQPTDLDREVFGPILHVV 926 
                                            **********************98876655555544.6799****************************** PP

                             TIGR01238  414 rykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGp 484 
                                            ryka+eld+++d+++a GygltlGvhsri+ t+++i +r  +Gn+yvnrn++GavvG qpfGG GlsGtGp
  NCBI__GCF_000427445.1:WP_026607825.1  927 RYKANELDRLLDQLEAMGYGLTLGVHSRIDATIAHIMERRLAGNCYVNRNMIGAVVGTQPFGGFGLSGTGP 997 
                                            *********************************************************************** PP

                             TIGR01238  485 kaGGplylyrlt 496 
                                            kaGGp+yl r+ 
  NCBI__GCF_000427445.1:WP_026607825.1  998 KAGGPHYLERFC 1009
                                            **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1032 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 53.72
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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