Alignments for a candidate for putA in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Sedimenticola selenatireducens DSM 17993

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_084610117.1 A3GO_RS0114220 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

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



>NCBI__GCF_000428045.1:WP_084610117.1
          Length = 1032

 Score = 1240 bits (3208), Expect = 0.0
 Identities = 637/1031 (61%), Positives = 781/1031 (75%), Gaps = 4/1031 (0%)

Query: 33   YIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQQYSLET 92
            Y VDE   L  LI L   + E +++ TR + ELV  VR  D    M  IDA L +YSL+T
Sbjct: 2    YCVDESSLLETLIPLARPTPELLKKTTRESAELVRAVRARDDAMHM--IDALLLEYSLDT 59

Query: 93   QEGIILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGLMLTGKI 152
            +EG++LMCLAE+L+RIPD+ATADALI+DKL  A W +HL +S S+LVNASTWGL+LTGK+
Sbjct: 60   REGVLLMCLAESLMRIPDSATADALIKDKLGIADWKQHLKQSKSLLVNASTWGLLLTGKV 119

Query: 153  VKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKNSEDKRK 212
            + LD  I+  P+++++RLVNRL EPV+RQAM  AMKIMG+QFVLGRT+ EAL NS  +R+
Sbjct: 120  ITLDAGIEDEPASVINRLVNRLSEPVVRQAMHQAMKIMGRQFVLGRTITEALANSRKQRE 179

Query: 213  LGYTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTISIKLSALHPRY 272
             GY++SYDMLGEAALT +DAE YF  Y+ AI  +G+ ++  + S R T+SIKLSALHPRY
Sbjct: 180  AGYSYSYDMLGEAALTDRDAEHYFEAYSGAIKAIGSDTFPSDTSFRSTVSIKLSALHPRY 239

Query: 273  EVANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWG 332
            E   E RV++EL D ++ LIKLAR L++GI+IDAEE DRLELSLKLF++L+    ++GWG
Sbjct: 240  EQQQERRVISELGDRMLALIKLARELDVGITIDAEEADRLELSLKLFERLYRDQISRGWG 299

Query: 333  LLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYT 392
             LG+VVQAY KRALPVL WL  LA +QGD IP+RL KGAYWDSE+K AQQ G  +YP++T
Sbjct: 300  NLGLVVQAYQKRALPVLFWLAALAGKQGDLIPLRLAKGAYWDSEIKHAQQLGLESYPVFT 359

Query: 393  RKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQRLHGMGQE 452
            RK  TDVSYLACA +LLSD  +G IYPQFASHNA TVA++  MA    +EFQRLHGMG  
Sbjct: 360  RKEATDVSYLACASFLLSDQLKGLIYPQFASHNAHTVASVVSMATHDQYEFQRLHGMGDA 419

Query: 453  LYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVVH 512
            LY+ ++ E  A  VRIYAP+G+HKDLLPYLVRRLLENGAN+SFVH+L+D KTP+ESL+ H
Sbjct: 420  LYEAVI-ERYASRVRIYAPVGSHKDLLPYLVRRLLENGANSSFVHRLIDQKTPVESLIEH 478

Query: 513  PLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAGP 572
            PL  L  Y +L+N +I LP DI+G  R NS G+N+N+  +  P    +  F    W A P
Sbjct: 479  PLTKLCQYSSLSNERIPLPPDIYGKGRINSCGVNINVADQWLPLQREVQAFFRQSWHAAP 538

Query: 573  LVNGQTL-TGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRAS 631
            L+ G+ + +GE   V +P D    VG +   D+  + QA+A A  AFA W  TPV  R+ 
Sbjct: 539  LIKGKRIESGEVVQVHAPHDRVIHVGSLIQTDEQTVGQAIAVACEAFAGWNATPVAKRSV 598

Query: 632  ALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLP 691
            AL++ ADLLEE+R ELIALC  EAGK+IQD IDEVREAVDFCRYYA QA+      +LL 
Sbjct: 599  ALERAADLLEEHRAELIALCHLEAGKTIQDAIDEVREAVDFCRYYAWQARLHFDSAQLLD 658

Query: 692  GPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAV 751
            GPTGE NEL+LQGRG+FVCISPWNFPLAIF GQV AALAAGN+V+AKPAEQTS+I  RAV
Sbjct: 659  GPTGEANELYLQGRGLFVCISPWNFPLAIFTGQVMAALAAGNSVIAKPAEQTSLIAARAV 718

Query: 752  QLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAII 811
            +L HQAGIP  VL  LPG G+ +G  LTADERI GV FTGST TA+LINR+LA R G + 
Sbjct: 719  ELFHQAGIPDSVLHLLPGEGSRIGPLLTADERIAGVAFTGSTETARLINRSLAMRNGPVA 778

Query: 812  PLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQ 871
             L+AETGGQNAMVVDST+ PEQV+ DV+SS+F SAGQRCSALRVLFLQ+D+A+R++ +L+
Sbjct: 779  TLVAETGGQNAMVVDSTALPEQVIKDVISSAFASAGQRCSALRVLFLQDDVAERILALLK 838

Query: 872  GAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMSLPAGTENGHFVS 931
            GAM EL +G+P  + TDVGPVID  A+  L  HI  +++   LI +  LP   E G FV+
Sbjct: 839  GAMAELKVGDPCELDTDVGPVIDEEARRTLQRHIAEMREQATLIAETPLPLNAEAGCFVA 898

Query: 932  PTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHALEV 991
            P A EI  +  L KEHFGP+LHVIR+KAS L  VI +IN++G+GLTLGIHSRNE  +  +
Sbjct: 899  PVAFEIQHMDQLSKEHFGPVLHVIRFKASRLDDVILQINNSGYGLTLGIHSRNETTSRYI 958

Query: 992  ADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIG 1051
              +V VGNVYINRNQIGAVVGVQPFGG GLSGTGPKAGGPHYL RF TE+TRT N TAIG
Sbjct: 959  DTRVRVGNVYINRNQIGAVVGVQPFGGLGLSGTGPKAGGPHYLLRFATERTRTTNTTAIG 1018

Query: 1052 GNATLLSLGDS 1062
            GNATLLSL +S
Sbjct: 1019 GNATLLSLENS 1029


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: 2422
Number of extensions: 91
Number of successful extensions: 4
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_084610117.1 A3GO_RS0114220 (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.20165.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-222  725.8   0.4   1.8e-222  725.1   0.4    1.3  1  lcl|NCBI__GCF_000428045.1:WP_084610117.1  A3GO_RS0114220 bifunctional prol


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_084610117.1  A3GO_RS0114220 bifunctional proline dehydrogenase/L-glutamate gamma-semiald
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.1   0.4  1.8e-222  1.8e-222       1     497 [.     499    1006 ..     499    1009 .. 0.98

  Alignments for each domain:
  == domain 1  score: 725.1 bits;  conditional E-value: 1.8e-222
                                 TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67  
                                                d+yg+gr ns Gv++++ ++  +l+ ++++   ++++aap++++k  ++ge+  v +p dr + vG 
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  499 DIYGKGRINSCGVNINVADQWLPLQREVQAFFRQSWHAAPLIKGKRIESGEVVQVHAPHDRVIHVGS 565 
                                                89***************************************************************** PP

                                 TIGR01238   68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134 
                                                + ++d+++v +a+  a +afa w+at+ ++r+  ler+adlle+h  el+al++ eaGkt+++ai+e
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  566 LIQTDEQTVGQAIAVACEAFAGWNATPVAKRSVALERAADLLEEHRAELIALCHLEAGKTIQDAIDE 632 
                                                ******************************************************************* PP

                                 TIGR01238  135 vreavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaG 188 
                                                vreavdf+ryya q++  +d                   +G +vcispwnfplaiftGq+ aalaaG
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  633 VREAVDFCRYYAWQARLHFDSAQLLDgptgeanelylqgRGLFVCISPWNFPLAIFTGQVMAALAAG 699 
                                                ***************99988875555789999*********************************** PP

                                 TIGR01238  189 ntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarli 255 
                                                n+viakpaeqtsliaaravel+++aG+p +v+ llpG G  +G  lt+deriaGv+ftGste+arli
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  700 NSVIAKPAEQTSLIAARAVELFHQAGIPDSVLHLLPGEGSRIGPLLTADERIAGVAFTGSTETARLI 766 
                                                ******************************************************************* PP

                                 TIGR01238  256 nkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrv 322 
                                                n++la r+ + ++l+aetGGqnam+vdstal+eqv++dv++saf+saGqrcsalrvl++q+dva+r+
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  767 NRSLAMRNGPVATLVAETGGQNAMVVDSTALPEQVIKDVISSAFASAGQRCSALRVLFLQDDVAERI 833 
                                                ******************************************************************* PP

                                 TIGR01238  323 ltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfva 389 
                                                l l+kGam elkvg p +l tdvGpvid+ea++ l++hi +m+++a  +a+  l    ++e g fva
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  834 LALLKGAMAELKVGDPCELDTDVGPVIDEEARRTLQRHIAEMREQATLIAETPLPL--NAEAGCFVA 898 
                                                *************************************************9998877..8999***** PP

                                 TIGR01238  390 ptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvG 456 
                                                p++fe++++d+l+ke fGpvlhv+r+ka++ld+v+ +in++GygltlG+hsr+e+t r+i++r++vG
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  899 PVAFEIQHMDQLSKEHFGPVLHVIRFKASRLDDVILQINNSGYGLTLGIHSRNETTSRYIDTRVRVG 965 
                                                ******************************************************************* PP

                                 TIGR01238  457 nvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                                nvy+nrn++GavvGvqpfGG GlsGtGpkaGGp+yl r+  
  lcl|NCBI__GCF_000428045.1:WP_084610117.1  966 NVYINRNQIGAVVGVQPFGGLGLSGTGPKAGGPHYLLRFAT 1006
                                                **************************************976 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 19.75
//
[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:

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