Alignments for a candidate for edd in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Halomonas desiderata SP1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_086509386.1 BZY95_RS07830 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_002151265.1:WP_086509386.1
          Length = 628

 Score =  780 bits (2013), Expect = 0.0
 Identities = 391/604 (64%), Positives = 473/604 (78%), Gaps = 6/604 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCG-SEDKHS 59
           ++  V +VTER+  RSR  R+ Y A +      G  RG+L C N AHG AGC  + DK  
Sbjct: 7   LNSTVEQVTERIRERSRGRRKLYEAHMAAQHQQGVHRGELSCGNLAHGFAGCDHAGDKDR 66

Query: 60  LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119
           L++ N+AN+AIVSSYNDMLSAH+P+E +PE IK+A R MGS  QFAGG PAMCDGVTQG 
Sbjct: 67  LKLTNSANLAIVSSYNDMLSAHRPFESYPEVIKQAARGMGSTAQFAGGVPAMCDGVTQGM 126

Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179
            GMELSL SR+VIA++TAVALSHNMFDAAL LGICDKIVPGL +GA RFGHLP +FVPGG
Sbjct: 127 PGMELSLFSRDVIAMATAVALSHNMFDAALYLGICDKIVPGLFIGAARFGHLPAVFVPGG 186

Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
           PMPSG+ N EKA +RQ YAEGK  REELLE+E +SYHSPGTCTFYGTAN+NQL+ME+MGL
Sbjct: 187 PMPSGLPNDEKARIRQLYAEGKVGREELLEAESRSYHSPGTCTFYGTANSNQLMMEMMGL 246

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
           HLPGASFVNP TPLR+ALT  A +Q  R T+QSGN+ P    +DER++VN++V L A+GG
Sbjct: 247 HLPGASFVNPGTPLREALTRYATEQAIRNTEQSGNYRPFYRQIDERAIVNAMVGLLASGG 306

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STNHTLH+ A+A AAGI + W D  DLS  VP+L+ +YPNG AD+NHFQAAGGM+ LIRE
Sbjct: 307 STNHTLHLVAMAAAAGITIDWNDFNDLSAAVPSLTRIYPNGSADVNHFQAAGGMSLLIRE 366

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           LL+AGL+H D+ TV G  L+ YTQEPFL++GKL WR+GP ESLD ++LRPV+  F+  GG
Sbjct: 367 LLDAGLIHGDIPTVFGTDLTAYTQEPFLEDGKLTWREGPTESLDSDVLRPVSNPFAATGG 426

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           L VMEGNLGRGV+K+SAV   +++VEAP  +F DQ  +  AF++GEL++D V V+RFQGP
Sbjct: 427 LVVMEGNLGRGVIKISAVKQANRVVEAPVRIFDDQNQVKAAFESGELDRDVVVVVRFQGP 486

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGK+PAAIHV+PEA   G LAR+R
Sbjct: 487 KANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVTPEAVDRGPLARLR 546

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAR---EPAKGLLGNNVGSGRELFGFMRMAFSSAEQG 596
           DGD++RVD  +G L   VDA EFA+R   EP   L   + G GRELFG  R   + AEQG
Sbjct: 547 DGDVVRVDAERGELTALVDAAEFASRGIVEP--NLERYHFGMGRELFGGFRHLAAGAEQG 604

Query: 597 ASAF 600
           A  F
Sbjct: 605 AGVF 608


Lambda     K      H
   0.318    0.134    0.386 

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: 1188
Number of extensions: 51
Number of successful extensions: 3
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: 608
Length of database: 628
Length adjustment: 37
Effective length of query: 571
Effective length of database: 591
Effective search space:   337461
Effective search space used:   337461
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: 53 (25.0 bits)

Align candidate WP_086509386.1 BZY95_RS07830 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

# 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/TIGR01196.hmm
# target sequence database:        /tmp/gapView.31577.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01196  [M=601]
Accession:   TIGR01196
Description: edd: phosphogluconate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-305  999.4   0.0   2.8e-305  999.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509386.1  BZY95_RS07830 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509386.1  BZY95_RS07830 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  999.2   0.0  2.8e-305  2.8e-305       1     600 [.       8     608 ..       8     609 .. 0.99

  Alignments for each domain:
  == domain 1  score: 999.2 bits;  conditional E-value: 2.8e-305
                                 TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalses.ekvelksekrknla 68 
                                               +s ++++teri ers+  r+ y +++ + +++g++r++l+cgnlahg+a ++++ +k  lk ++ +nla
  lcl|NCBI__GCF_002151265.1:WP_086509386.1   8 NSTVEQVTERIRERSRGRRKLYEAHMAAQHQQGVHRGELSCGNLAHGFAGCDHAgDKDRLKLTNSANLA 76 
                                               5789***********************************************9764899*********** PP

                                 TIGR01196  69 iitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstai 137
                                               i+++yndmlsah+pf++yp++ik+a++  +++aq agGvpamcdGvtqG +Gmelsl+srdvia++ta+
  lcl|NCBI__GCF_002151265.1:WP_086509386.1  77 IVSSYNDMLSAHRPFESYPEVIKQAARGMGSTAQFAGGVPAMCDGVTQGMPGMELSLFSRDVIAMATAV 145
                                               ********************************************************************* PP

                                 TIGR01196 138 glshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreel 206
                                               +lshnmfd+al+lG+cdkivpGl i+a+ fGhlpavfvp+Gpm+sGl+n+eka++rql+aeGkv+reel
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 146 ALSHNMFDAALYLGICDKIVPGLFIGAARFGHLPAVFVPGGPMPSGLPNDEKARIRQLYAEGKVGREEL 214
                                               ********************************************************************* PP

                                 TIGR01196 207 lksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevl 275
                                               l++e++syh+pGtctfyGtansnq+++e+mGlhlpgasfvnp tplr+altr+a++++ r t ++g++ 
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 215 LEAESRSYHSPGTCTFYGTANSNQLMMEMMGLHLPGASFVNPGTPLREALTRYATEQAIRNTEQSGNYR 283
                                               ********************************************************************* PP

                                 TIGR01196 276 plaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvn 344
                                               p+ + ide++ivna+vglla+GGstnhtlhlva+a aaGi ++w+d+++ls  vp l+r+ypnG+advn
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 284 PFYRQIDERAIVNAMVGLLASGGSTNHTLHLVAMAAAAGITIDWNDFNDLSAAVPSLTRIYPNGSADVN 352
                                               ********************************************************************* PP

                                 TIGR01196 345 hfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpf 413
                                               hf+aaGG+s+lirell++Gl+h d+ tv g+ l +yt+epfledgkl++re++ +sld+d+lr+v++pf
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 353 HFQAAGGMSLLIRELLDAGLIHGDIPTVFGTDLTAYTQEPFLEDGKLTWREGPTESLDSDVLRPVSNPF 421
                                               ********************************************************************* PP

                                 TIGR01196 414 saeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanG 482
                                               +a+GGl +++GnlGr+vik+savk+ +rv+eap+++f+dq++++aaf++gel+rd+v+vvrfqGpkanG
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 422 AATGGLVVMEGNLGRGVIKISAVKQANRVVEAPVRIFDDQNQVKAAFESGELDRDVVVVVRFQGPKANG 490
                                               ********************************************************************* PP

                                 TIGR01196 483 mpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavnge 551
                                               mpelhklt++lGvlqdrg+kvalvtdGr+sGasGkvpaaihvtpea++ G+la++rdGd++r+da  ge
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 491 MPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVTPEAVDRGPLARLRDGDVVRVDAERGE 559
                                               ********************************************************************* PP

                                 TIGR01196 552 levlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                               l+ lvd ae+++r + e++le  ++G+Grelf  +r+ +++ae+Ga ++
  lcl|NCBI__GCF_002151265.1:WP_086509386.1 560 LTALVDAAEFASRGIVEPNLERYHFGMGRELFGGFRHLAAGAEQGAGVF 608
                                               **********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (628 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.06
# Mc/sec: 6.25
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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