Alignments for a candidate for edd in Methylococcus capsulatus Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Methylococcus capsulatus Bath

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_010959409.1 MCA_RS00185 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000008325.1:WP_010959409.1
          Length = 609

 Score =  738 bits (1906), Expect = 0.0
 Identities = 371/601 (61%), Positives = 450/601 (74%), Gaps = 2/601 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +H  +++VT+R+ ARS   R AYL L+  A   G +R  + C N AH  A   + DK  L
Sbjct: 3   LHQTLVDVTDRIRARSHDRRAAYLDLMHRARQKGVERSHIACTNVAHAYAATPANDKLVL 62

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           +     N+ IV++YNDMLSAHQPYE +PE IK   R  G   Q AGG PAMCDGVTQG+ 
Sbjct: 63  KAATVPNLGIVTAYNDMLSAHQPYERYPEIIKDEARRAGVTAQVAGGVPAMCDGVTQGQT 122

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIALSTAVALSH +FDA L LG+CDKIVPGL++ ALRFGHLP +FVP GP
Sbjct: 123 GMELSLFSRDVIALSTAVALSHRVFDANLYLGVCDKIVPGLLIAALRFGHLPGVFVPAGP 182

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISN EKA VRQ++AEGK  R+ LLESEM SYHS GTCTFYGTAN+NQ+L+E+MGL 
Sbjct: 183 MVSGISNSEKAKVRQQFAEGKVGRDALLESEMASYHSAGTCTFYGTANSNQMLLEIMGLQ 242

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP TPLRDALT  A +    L + +     +  IVDER +VN+IV L ATGGS
Sbjct: 243 LPGSSFVNPGTPLRDALTRAATRVAVDLARDA-TAPALCHIVDERVIVNAIVGLLATGGS 301

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHT+H+ AIA+AAGI++ W D  DLS VVP L+ VYPNGKAD+NHF AAGGM FL+REL
Sbjct: 302 TNHTIHLVAIARAAGIEVNWDDFNDLSAVVPLLARVYPNGKADVNHFHAAGGMGFLVREL 361

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGLLHEDV T+ G GL R+ +EP+LDNG L WRD P +S D  +L P    FSP+GGL
Sbjct: 362 LDAGLLHEDVQTILGPGLRRWAEEPWLDNGTLAWRDAPEKSHDPEVLAPAGEPFSPDGGL 421

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R++ GN+GRGV+KVSAVA ++++V APA+VF+ Q +L  AFK GELE+DFVAV+RFQGPR
Sbjct: 422 RLVTGNIGRGVIKVSAVAPENRVVRAPAIVFESQDELIAAFKRGELERDFVAVLRFQGPR 481

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELH++TP L  LQDRGFKVAL+TDGRMSGASGK+PAAIH+SPEA +GG L  +R 
Sbjct: 482 ANGMPELHQLTPALASLQDRGFKVALITDGRMSGASGKVPAAIHISPEAAMGGPLTLLRT 541

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           GD I +D V+G LE +V AD +A REP    L GN  G GRELF   R    + E+GA  
Sbjct: 542 GDTILLDAVRGKLEAEVPADRWALREPVTDDLSGNRFGCGRELFSGFRHLADTPERGAFT 601

Query: 600 F 600
           F
Sbjct: 602 F 602


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: 1154
Number of extensions: 61
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: 609
Length adjustment: 37
Effective length of query: 571
Effective length of database: 572
Effective search space:   326612
Effective search space used:   326612
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_010959409.1 MCA_RS00185 (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.19400.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-303  991.5   0.0     7e-303  991.3   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010959409.1  MCA_RS00185 phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010959409.1  MCA_RS00185 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  991.3   0.0    7e-303    7e-303       2     600 ..       5     602 ..       4     603 .. 0.99

  Alignments for each domain:
  == domain 1  score: 991.3 bits;  conditional E-value: 7e-303
                                 TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaii 70 
                                                 l+++t+ri +rs++ r +yl+ ++ a++kg+ rs+++c+n+ah++aa + ++k+ lk  +++nl+i+
  lcl|NCBI__GCF_000008325.1:WP_010959409.1   5 QTLVDVTDRIRARSHDRRAAYLDLMHRARQKGVERSHIACTNVAHAYAATPANDKLVLKAATVPNLGIV 73 
                                               67899**************************************************************** PP

                                 TIGR01196  71 tayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaigl 139
                                               tayndmlsahqp+++yp++ik+++++a+ +aqvagGvpamcdGvtqG+ Gmelsl+srdvialsta++l
  lcl|NCBI__GCF_000008325.1:WP_010959409.1  74 TAYNDMLSAHQPYERYPEIIKDEARRAGVTAQVAGGVPAMCDGVTQGQTGMELSLFSRDVIALSTAVAL 142
                                               ********************************************************************* PP

                                 TIGR01196 140 shnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellk 208
                                               sh++fd+ l+lGvcdkivpGlliaal fGhlp+vfvpaGpm+sG++n+ekakvrq+faeGkv+r++ll+
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 143 SHRVFDANLYLGVCDKIVPGLLIAALRFGHLPGVFVPAGPMVSGISNSEKAKVRQQFAEGKVGRDALLE 211
                                               ********************************************************************* PP

                                 TIGR01196 209 semasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlpl 277
                                               semasyh++GtctfyGtansnqml+e+mGl+lpg+sfvnp tplrdaltr+a++ +    a++++   l
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 212 SEMASYHSAGTCTFYGTANSNQMLLEIMGLQLPGSSFVNPGTPLRDALTRAATRVAVD-LARDATAPAL 279
                                               **************************************************99887777.679999999* PP

                                 TIGR01196 278 aelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhf 346
                                               ++++de++ivna+vgllatGGstnht+hlvaiaraaGi +nwdd+++ls +vpllarvypnGkadvnhf
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 280 CHIVDERVIVNAIVGLLATGGSTNHTIHLVAIARAAGIEVNWDDFNDLSAVVPLLARVYPNGKADVNHF 348
                                               ********************************************************************* PP

                                 TIGR01196 347 eaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsa 415
                                               +aaGG++fl+rell++Gllhedv+t++g Glrr+++ep+l++g l +r+a+eks d ++l+++ +pfs+
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 349 HAAGGMGFLVRELLDAGLLHEDVQTILGPGLRRWAEEPWLDNGTLAWRDAPEKSHDPEVLAPAGEPFSP 417
                                               ********************************************************************* PP

                                 TIGR01196 416 eGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmp 484
                                               +GGl+l+ Gn+Gr+vikvsav++e+rv++apaivf++q el+aafk+gelerd+vav+rfqGp+anGmp
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 418 DGGLRLVTGNIGRGVIKVSAVAPENRVVRAPAIVFESQDELIAAFKRGELERDFVAVLRFQGPRANGMP 486
                                               ********************************************************************* PP

                                 TIGR01196 485 elhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553
                                               elh+lt++l  lqdrgfkval+tdGr+sGasGkvpaaih++pea++gG+l+ +r+Gd i ldav g+le
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 487 ELHQLTPALASLQDRGFKVALITDGRMSGASGKVPAAIHISPEAAMGGPLTLLRTGDTILLDAVRGKLE 555
                                               ********************************************************************* PP

                                 TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                                 v    ++ re+ + dl+ n++G+Grelf+ +r+ +++ e+Ga ++
  lcl|NCBI__GCF_000008325.1:WP_010959409.1 556 AEVPADRWALREPVTDDLSGNRFGCGRELFSGFRHLADTPERGAFTF 602
                                               ********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (609 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.71
//
[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