Alignments for a candidate for putA in Malonomonas rubra DSM 5091

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Malonomonas rubra DSM 5091

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_072908502.1 BUB13_RS10015 L-glutamate gamma-semialdehyde dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>NCBI__GCF_900142125.1:WP_072908502.1
          Length = 549

 Score =  526 bits (1356), Expect = e-154
 Identities = 264/542 (48%), Positives = 363/542 (66%), Gaps = 5/542 (0%)

Query: 28  ATYKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSN 87
           A   +P   NEP   YA G+P+R+ L++AL    ++  + VPL+I GKEV++ ++   + 
Sbjct: 7   AVINIPTPVNEPVLSYAPGTPERQKLKDALEEL-KSQQIEVPLIIGGKEVRTGNTAKIAC 65

Query: 88  PASHG-PVATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDV 146
           P  H   +  Y  A  K+VQ AI++A+ A+  W S  + +R+++FLKAADL+S  YR+ +
Sbjct: 66  PHDHSIELGQYHKAGPKEVQMAIDAAMAAKPVWESLRWEERSAIFLKAADLLSGPYRFLI 125

Query: 147 MALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEG 206
            A TM    KN +QAEIDSA EL DF RF V +A ++Y +QP++ +  +WN V++RPLEG
Sbjct: 126 NAATMLNISKNPFQAEIDSACELIDFLRFNVFFASEIYREQPMYSSKDIWNYVQHRPLEG 185

Query: 207 FVYAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFV 266
           FV+A++PFNFTAI GNL  +PA+MGN VVWKP+ SA+ + +   ++L EAGLP  VI FV
Sbjct: 186 FVFAVAPFNFTAISGNLPTSPAIMGNTVVWKPASSAVFAPYYFMKLLQEAGLPDGVINFV 245

Query: 267 PGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNF 326
           PG   +V  T+L  PDF  +HFTGST VF++++ +I   +A   Y++YPRIVGETGGK+F
Sbjct: 246 PGSGSDVGDTILASPDFNGIHFTGSTPVFQSMWKEIGANLAKDHYKTYPRIVGETGGKDF 305

Query: 327 HLIHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPP 386
              H SA++   A   VRGAFEYQGQKCSA SR Y+  S+ D+ L +V ++   +K G  
Sbjct: 306 IFAHSSANVAALATAMVRGAFEYQGQKCSAASRTYLPESLKDAVLAEVKNQVSRIKTGDV 365

Query: 387 SDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDH 446
            DF NF   VI + +F  + + ID AK   + E++ GG YD SKGW+I+PT+  TTNP  
Sbjct: 366 CDFGNFFNAVIDKGAFKSITEYIDYAKTADDAEIVIGGGYDDSKGWFIEPTLIVTTNPKF 425

Query: 447 PLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLR 506
             +  E+FGP+L VY YPD   A++ +  +  D T  + LTG+VFAQ+R A+++A   L 
Sbjct: 426 KTMEEEIFGPVLTVYCYPD---AEYEQTLELCDQTSPFSLTGAVFAQERTAISLALTKLE 482

Query: 507 NAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVA 566
           NA+GNFYIN K TGAVVGQQPFGG RASGTNDKAGS   L R+ S+R+IKE FVP     
Sbjct: 483 NASGNFYINDKPTGAVVGQQPFGGGRASGTNDKAGSKQNLMRWASVRTIKENFVPPTSFE 542

Query: 567 YP 568
           YP
Sbjct: 543 YP 544


Lambda     K      H
   0.316    0.130    0.379 

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: 888
Number of extensions: 40
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: 572
Length of database: 549
Length adjustment: 36
Effective length of query: 536
Effective length of database: 513
Effective search space:   274968
Effective search space used:   274968
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: 53 (25.0 bits)

Align candidate WP_072908502.1 BUB13_RS10015 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.508896.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-235  768.5   0.0   2.1e-235  768.3   0.0    1.0  1  NCBI__GCF_900142125.1:WP_072908502.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072908502.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.3   0.0  2.1e-235  2.1e-235       2     531 ..      16     545 ..      15     547 .. 0.99

  Alignments for each domain:
  == domain 1  score: 768.3 bits;  conditional E-value: 2.1e-235
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           nePv +++pg++er++l+ +l+elks+++e+Pl+iggkev + +++ ++  P+dh+ +l++ ++a++++v+ a
  NCBI__GCF_900142125.1:WP_072908502.1  16 NEPVLSYAPGTPERQKLKDALEELKSQQIEVPLIIGGKEVRT-GNTAKIACPHDHSIELGQYHKAGPKEVQMA 87 
                                           9**************************************655.558*************************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           ++aa++ak  W++l +++r+aiflkaadllsg+yr  i+aatml+ sk+++qaeid+++elidf+rfnv +a+
  NCBI__GCF_900142125.1:WP_072908502.1  88 IDAAMAAKPVWESLRWEERSAIFLKAADLLSGPYRFLINAATMLNISKNPFQAEIDSACELIDFLRFNVFFAS 160
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           e++  qP  s++  +n v++rpleGfv+a++Pfnftai++nl+++Pa+mGn+vvWkP++ av++ y  mk+l+
  NCBI__GCF_900142125.1:WP_072908502.1 161 EIYREQPMYSSKDIWNYVQHRPLEGFVFAVAPFNFTAISGNLPTSPAIMGNTVVWKPASSAVFAPYYFMKLLQ 233
                                           ************************************************************************* PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldk..yrnfPrivGetGGkdfv 291
                                           eaGlP gvinfvp+ g  v+d++la++d+ ++hftGst+vf+++wk++  nl k  y+++PrivGetGGkdf+
  NCBI__GCF_900142125.1:WP_072908502.1 234 EAGLPDGVINFVPGSGSDVGDTILASPDFNGIHFTGSTPVFQSMWKEIGANLAKdhYKTYPRIVGETGGKDFI 306
                                           ****************************************************8878***************** PP

                             TIGR01236 292 lvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavidek 364
                                           ++h+sa+v  +++a++rgafeyqGqkcsaasr y+p+sl + + +e++++ +++k gdv d+ +f+ avid+ 
  NCBI__GCF_900142125.1:WP_072908502.1 307 FAHSSANVAALATAMVRGAFEYQGQKCSAASRTYLPESLKDAVLAEVKNQVSRIKTGDVCDFGNFFNAVIDKG 379
                                           ************************************************************************* PP

                             TIGR01236 365 sfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeil 437
                                           +f+ i ++i++ak+ +++ ei++GG yddskG+f+ePt++ + +Pk k+m+eeifGPvltvy y+d +y+++l
  NCBI__GCF_900142125.1:WP_072908502.1 380 AFKSITEYIDYAKT-ADDAEIVIGGGYDDSKGWFIEPTLIVTTNPKFKTMEEEIFGPVLTVYCYPDAEYEQTL 451
                                           *************9.669******************************************************* PP

                             TIGR01236 438 evvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillr 510
                                           e+ d+ts ++ltGavfa++r ai  a  kl +a+Gnfyindk+tGavvgqqpfGG r+sGtndkaG+ ++l+r
  NCBI__GCF_900142125.1:WP_072908502.1 452 ELCDQTSPFSLTGAVFAQERTAISLALTKLENASGNFYINDKPTGAVVGQQPFGGGRASGTNDKAGSKQNLMR 524
                                           ************************************************************************* PP

                             TIGR01236 511 fvsarsiketfkeltdfkypy 531
                                           + s+r+ike+f+++t f+yp+
  NCBI__GCF_900142125.1:WP_072908502.1 525 WASVRTIKENFVPPTSFEYPF 545
                                           *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (549 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.45
//
[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