Alignments for a candidate for edd in Halomonas xinjiangensis TRM 0175

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Halomonas xinjiangensis TRM 0175

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_043527536.1 JH15_RS04900 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000759345.1:WP_043527536.1
          Length = 629

 Score =  762 bits (1968), Expect = 0.0
 Identities = 376/602 (62%), Positives = 468/602 (77%), Gaps = 2/602 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSE-DKHS 59
           +H  V  VT R+  RS   R+ Y   +      G  RG+L C N AHG AGC    DK  
Sbjct: 8   LHETVDRVTRRIRERSSHRRDLYEQHMEEQHRQGVHRGELSCGNLAHGFAGCDHPGDKDR 67

Query: 60  LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119
           L++ N+AN+ IVSSYNDMLSAH+P+E +P  IK+A R MGS  QFAGG PAMCDGVTQG+
Sbjct: 68  LKLTNSANLGIVSSYNDMLSAHRPFEDYPATIKEAARGMGSTAQFAGGVPAMCDGVTQGQ 127

Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179
            GMELSL SR+VIA++TAVALSHNMFDAAL LGICDKIVPGL +GA RFGHLP +FVPGG
Sbjct: 128 PGMELSLFSRDVIAMATAVALSHNMFDAALYLGICDKIVPGLFIGAARFGHLPAVFVPGG 187

Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
           PM SG+ N EKA VRQ YAEGKA+RE+LLE+E +SYHSPGTCTFYGTAN+NQL+ME+MGL
Sbjct: 188 PMTSGLPNNEKARVRQLYAEGKASREDLLEAESQSYHSPGTCTFYGTANSNQLMMEMMGL 247

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
           HLPGASFVNP TP+RDALT  A +Q  R T+QSG++ P  + +DER++VN++V L A+GG
Sbjct: 248 HLPGASFVNPGTPIRDALTRYATEQAIRNTEQSGDYRPFYKQIDERAIVNAMVGLLASGG 307

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STNHTLH+ A+A AAG+ +TW D  +LS V+P+++ +YPNG+AD+NHFQAAGGM+ LIRE
Sbjct: 308 STNHTLHLVAMAAAAGLTITWDDFTELSAVIPSMTRIYPNGQADVNHFQAAGGMSLLIRE 367

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L+ AGL+H D+ TV G  L+ YTQEPFL++GKLVWR+GP +S D ++LRPVA  FSP GG
Sbjct: 368 LIGAGLIHADIPTVFGTDLTAYTQEPFLEDGKLVWREGPAQSHDLDVLRPVAEPFSPTGG 427

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           L V++GNLGRGV+KVSAV  +H++VEAP  +F DQ  +  AF++GEL++D V V+RFQGP
Sbjct: 428 LTVLDGNLGRGVIKVSAVKQEHRVVEAPVRIFNDQNQVKAAFESGELDRDVVVVVRFQGP 487

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGK+PAAIH++PEA   G LA+++
Sbjct: 488 KANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHITPEAIDRGPLAKLK 547

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPA-KGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           DGD++R+D  KG L   VD  E + R      L  N+ G GRELF   R   + AE+GA 
Sbjct: 548 DGDVVRLDTDKGELRALVDDAELSGRPLLDPNLEHNHFGMGRELFSGFRHLAAGAEEGAG 607

Query: 599 AF 600
            F
Sbjct: 608 VF 609


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: 1180
Number of extensions: 48
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: 629
Length adjustment: 37
Effective length of query: 571
Effective length of database: 592
Effective search space:   338032
Effective search space used:   338032
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_043527536.1 JH15_RS04900 (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.1361035.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   2.9e-305  999.2   0.0    1.0  1  NCBI__GCF_000759345.1:WP_043527536.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043527536.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  999.2   0.0  2.9e-305  2.9e-305       2     600 ..      10     609 ..       9     610 .. 0.99

  Alignments for each domain:
  == domain 1  score: 999.2 bits;  conditional E-value: 2.9e-305
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaals.esekvelksekrknlaiitay 73 
                                             + ++t+ri ers + r+ y +++++ +++g++r++l+cgnlahg+a ++ + +k  lk ++ +nl+i+++y
  NCBI__GCF_000759345.1:WP_043527536.1  10 ETVDRVTRRIRERSSHRRDLYEQHMEEQHRQGVHRGELSCGNLAHGFAGCDhPGDKDRLKLTNSANLGIVSSY 82 
                                           56899*********************************************73579****************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsah+pf++yp+ ik+a++  +++aq agGvpamcdGvtqG++Gmelsl+srdvia++ta++lshnmfd+
  NCBI__GCF_000759345.1:WP_043527536.1  83 NDMLSAHRPFEDYPATIKEAARGMGSTAQFAGGVPAMCDGVTQGQPGMELSLFSRDVIAMATAVALSHNMFDA 155
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           al+lG+cdkivpGl i+a+ fGhlpavfvp+Gpm+sGl+n+eka+vrql+aeGk++re+ll++e++syh+pGt
  NCBI__GCF_000759345.1:WP_043527536.1 156 ALYLGICDKIVPGLFIGAARFGHLPAVFVPGGPMTSGLPNNEKARVRQLYAEGKASREDLLEAESQSYHSPGT 228
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtansnq+++e+mGlhlpgasfvnp tp+rdaltr+a++++ r t ++g++ p+ + ide++ivna+vg
  NCBI__GCF_000759345.1:WP_043527536.1 229 CTFYGTANSNQLMMEMMGLHLPGASFVNPGTPIRDALTRYATEQAIRNTEQSGDYRPFYKQIDERAIVNAMVG 301
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           lla+GGstnhtlhlva+a aaG+ ++wdd+ els ++p ++r+ypnG+advnhf+aaGG+s+lirel+ +Gl+
  NCBI__GCF_000759345.1:WP_043527536.1 302 LLASGGSTNHTLHLVAMAAAAGLTITWDDFTELSAVIPSMTRIYPNGQADVNHFQAAGGMSLLIRELIGAGLI 374
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438
                                           h d+ tv g+ l +yt+epfledgkl++re++ +s d d+lr+v +pfs++GGl +l+GnlGr+vikvsavk+
  NCBI__GCF_000759345.1:WP_043527536.1 375 HADIPTVFGTDLTAYTQEPFLEDGKLVWREGPAQSHDLDVLRPVAEPFSPTGGLTVLDGNLGRGVIKVSAVKQ 447
                                           ************************************************************************* PP

                             TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511
                                           e+rv+eap+++f+dq++++aaf++gel+rd+v+vvrfqGpkanGmpelhklt++lGvlqdrg+kvalvtdGr+
  NCBI__GCF_000759345.1:WP_043527536.1 448 EHRVVEAPVRIFNDQNQVKAAFESGELDRDVVVVVRFQGPKANGMPELHKLTPFLGVLQDRGYKVALVTDGRM 520
                                           ************************************************************************* PP

                             TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfa 584
                                           sGasGkvpaaih+tpea++ G+lak++dGd++rld+ +gel+ lvddael  r l  ++le+n++G+Grelf+
  NCBI__GCF_000759345.1:WP_043527536.1 521 SGASGKVPAAIHITPEAIDRGPLAKLKDGDVVRLDTDKGELRALVDDAELSGRPLLDPNLEHNHFGMGRELFS 593
                                           ************************************************************************* PP

                             TIGR01196 585 alrekvssaeeGassl 600
                                            +r+ +++aeeGa ++
  NCBI__GCF_000759345.1:WP_043527536.1 594 GFRHLAAGAEEGAGVF 609
                                           *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (629 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: 00:00:00.01
# Mc/sec: 31.15
//
[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 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