Alignments for a candidate for edd in Methylovulum miyakonense HT12

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Methylovulum miyakonense HT12

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_019865040.1 METMI_RS0104465 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000384075.1:WP_019865040.1
          Length = 606

 Score =  741 bits (1913), Expect = 0.0
 Identities = 360/600 (60%), Positives = 455/600 (75%), Gaps = 2/600 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHP + +VT+ ++ RS  TREAYL  I GA   GP R  L C N AHG A CG+ +K  L
Sbjct: 1   MHPLLEKVTKEVIDRSHRTREAYLVCIDGAIGKGPHRSVLGCGNLAHGFAACGAGEKLDL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
                AN+ I+SSYNDMLSAH+PY+  P  IK+A+   G V QFAGG PAMCDG+TQG+A
Sbjct: 61  AGDKKANIGIISSYNDMLSAHEPYKDAPALIKEAISAAGGVAQFAGGVPAMCDGITQGQA 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIA+STA+ LSHNMFD AL LG+CDKIVPGL+MGAL FGHLP +FVP GP
Sbjct: 121 GMELSLFSRDVIAMSTAIGLSHNMFDGALYLGVCDKIVPGLLMGALSFGHLPAVFVPAGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGI+NKEK+  RQ+YAEGK  R ELLESE KSYHSPGTCTFYGTAN+NQ+++E+MGLH
Sbjct: 181 MPSGITNKEKSRARQQYAEGKIGRAELLESESKSYHSPGTCTFYGTANSNQMMVEMMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNPYTPLRD LT  AA+QV + T    +F PIG +++E++++N+++ L ATGGS
Sbjct: 241 LPGSSFVNPYTPLRDELTKAAARQVLKFTALGNDFRPIGHVINEKAILNALIGLLATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHT+H+ AIA+ AGI + W D  +LS+ +P ++ +YPNG AD+NHFQAAGGM  LI EL
Sbjct: 301 TNHTMHLVAIARMAGIIINWNDFDNLSKAIPLITKIYPNGPADVNHFQAAGGMGVLIAEL 360

Query: 361 LEAGLLHEDVNTVAGR-GLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L+ G++HED+ T+  R G+ +YTQEP +  G LVW   P  SLD  ++  V + F+P GG
Sbjct: 361 LKHGMMHEDILTIGDRHGMGQYTQEPKIIGGNLVWEASPAASLDTEVIATVEKPFAPGGG 420

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           + ++ GNLGRG+ KVSAV+  HQ+VEAPAVVF DQ ++  AFK GEL  DFVAV+RFQGP
Sbjct: 421 IHLIRGNLGRGISKVSAVSEDHQVVEAPAVVFDDQDEMMAAFKRGELNHDFVAVLRFQGP 480

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           R+NGMPELHK+TP LG+LQD+G+KVAL+TDGRMSGASGK+P+AIH+ PE   GG LA+VR
Sbjct: 481 RANGMPELHKLTPALGLLQDKGYKVALLTDGRMSGASGKVPSAIHMYPECINGGPLAKVR 540

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKGLLGN-NVGSGRELFGFMRMAFSSAEQGAS 598
           +GDII ++   G + + VD  EF  R P +    N + G GRE+FG  R   ++AE GAS
Sbjct: 541 NGDIISLNIKTGDVNVLVDETEFNGRLPEENSAKNHHFGMGREMFGGFRQGATTAETGAS 600


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: 1157
Number of extensions: 49
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: 606
Length adjustment: 37
Effective length of query: 571
Effective length of database: 569
Effective search space:   324899
Effective search space used:   324899
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_019865040.1 METMI_RS0104465 (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.3921166.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-305  998.2   0.6   6.6e-305  998.0   0.6    1.0  1  NCBI__GCF_000384075.1:WP_019865040.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000384075.1:WP_019865040.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  998.0   0.6  6.6e-305  6.6e-305       1     600 [.       2     602 ..       2     603 .. 0.99

  Alignments for each domain:
  == domain 1  score: 998.0 bits;  conditional E-value: 6.6e-305
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h+ l+++t+ +i+rs++tre+yl  i  a  kg++rs+lgcgnlahg+aa+   ek++l+ +k++n++ii++y
  NCBI__GCF_000384075.1:WP_019865040.1   2 HPLLEKVTKEVIDRSHRTREAYLVCIDGAIGKGPHRSVLGCGNLAHGFAACGAGEKLDLAGDKKANIGIISSY 74 
                                           67799******************************************************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsah+p+k+ p+lik+a+  a++vaq agGvpamcdG+tqG++Gmelsl+srdvia+staiglshnmfdg
  NCBI__GCF_000384075.1:WP_019865040.1  75 NDMLSAHEPYKDAPALIKEAISAAGGVAQFAGGVPAMCDGITQGQAGMELSLFSRDVIAMSTAIGLSHNMFDG 147
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           al+lGvcdkivpGll++alsfGhlpavfvpaGpm+sG++nkek+++rq++aeGk++r ell+se++syh+pGt
  NCBI__GCF_000384075.1:WP_019865040.1 148 ALYLGVCDKIVPGLLMGALSFGHLPAVFVPAGPMPSGITNKEKSRARQQYAEGKIGRAELLESESKSYHSPGT 220
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtansnqm+ve+mGlhlpg+sfvnp+tplrd+lt++aa+++ + ta ++++ p++++i+ek+i+nal+g
  NCBI__GCF_000384075.1:WP_019865040.1 221 CTFYGTANSNQMMVEMMGLHLPGSSFVNPYTPLRDELTKAAARQVLKFTALGNDFRPIGHVINEKAILNALIG 293
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           llatGGstnht+hlvaiar aGii+nw+d+++ls+ +pl++++ypnG advnhf+aaGG+++li+ellk+G++
  NCBI__GCF_000384075.1:WP_019865040.1 294 LLATGGSTNHTMHLVAIARMAGIIINWNDFDNLSKAIPLITKIYPNGPADVNHFQAAGGMGVLIAELLKHGMM 366
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvag.kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           hed+ t+ + +G+ +yt+ep++  g+l+++ ++ +sld++++++v+kpf++ GG++l++GnlGr++ kvsav 
  NCBI__GCF_000384075.1:WP_019865040.1 367 HEDILTIGDrHGMGQYTQEPKIIGGNLVWEASPAASLDTEVIATVEKPFAPGGGIHLIRGNLGRGISKVSAVS 439
                                           *******9989************************************************************** PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                           e+++v+eapa+vf+dq e++aafk+gel++d+vav+rfqGp+anGmpelhklt++lG+lqd+g+kval+tdGr
  NCBI__GCF_000384075.1:WP_019865040.1 440 EDHQVVEAPAVVFDDQDEMMAAFKRGELNHDFVAVLRFQGPRANGMPELHKLTPALGLLQDKGYKVALLTDGR 512
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           +sGasGkvp+aih+ pe+++gG+lak+r+Gd+i l+ ++g+++vlvd++e++ r +ee   ++ ++G+Gre+f
  NCBI__GCF_000384075.1:WP_019865040.1 513 MSGASGKVPSAIHMYPECINGGPLAKVRNGDIISLNIKTGDVNVLVDETEFNGRLPEENSAKNHHFGMGREMF 585
                                           ************************************************************************* PP

                             TIGR01196 584 aalrekvssaeeGassl 600
                                             +r+ +++ae+Gas l
  NCBI__GCF_000384075.1:WP_019865040.1 586 GGFRQGATTAETGASNL 602
                                           **************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (606 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: 00:00:00.00
# Mc/sec: 39.93
//
[ok]

This GapMind analysis is from Apr 09 2024. 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