Alignments for a candidate for edd in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Herbaspirillum seropedicae SmR1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__HerbieS:HSERO_RS05520
          Length = 623

 Score =  746 bits (1925), Expect = 0.0
 Identities = 367/608 (60%), Positives = 462/608 (75%), Gaps = 8/608 (1%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  +  VT+R+  RSR  R AYL  +  A   G QRG L C N AHG A   + DK  L
Sbjct: 3   LNATLASVTQRIAERSRPYRTAYLERLEAARRKGAQRGALACTNLAHGFAAFPANDKLKL 62

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           +   A ++AIVS+YNDMLSAHQP+E FP+ IK A RE G+V QFAGG+PAMCDGVTQG+A
Sbjct: 63  KEDKAPSLAIVSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQA 122

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+ IA++TA+ALSHNMFDAAL LG+CDKIVPGL++GAL FGHLP +FVP GP
Sbjct: 123 GMELSLFSRDAIAMATAIALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGP 182

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG+SN +K  +RQ Y  GK  R ELLE+E KSYH  GTCTFYGTAN+NQ+LME MGLH
Sbjct: 183 MTSGMSNSDKVKIRQLYTAGKIGRAELLEAESKSYHGAGTCTFYGTANSNQMLMEAMGLH 242

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGA+F+ P TPLRDALT  AA+Q  ++T     +TP+G ++DE+S+VN+IVALHATGGS
Sbjct: 243 LPGAAFITPNTPLRDALTAAAAKQAAKITDLGTQYTPVGRMIDEKSIVNAIVALHATGGS 302

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLH+ AIA+AAGI + W D   LS VVP ++ +YPNG AD+NHF AAGG  F++REL
Sbjct: 303 TNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTADVNHFHAAGGTGFVLREL 362

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFL----DNGK---LVWRDGPIESLDENILRPVARA 413
           ++AGL+H+DV T+ G+GL ++ +EP L    +NG+   + W D P +S DE +L  VA+ 
Sbjct: 363 IDAGLMHDDVTTILGQGLRQHCKEPMLAAEGENGRPGIVTWHDAPAQSGDEGVLGTVAKP 422

Query: 414 FSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAV 473
           F+ +GGL++++GNLGR V+K+SAV  +H++VEAPAVVF  Q+    AFKAG+L++DFVAV
Sbjct: 423 FAADGGLKLLQGNLGRAVIKISAVKPEHRVVEAPAVVFHSQEAFMAAFKAGQLDRDFVAV 482

Query: 474 MRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGG 533
           + FQGPR+NGMPELH +TP LG+LQD+G  VALVTDGRMSGASGK+PAAIHV+PE   GG
Sbjct: 483 ITFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGG 542

Query: 534 ALARVRDGDIIRVDGVKGTLELKVDADEFAAR-EPAKGLLGNNVGSGRELFGFMRMAFSS 592
            L RVRDGDIIR+D   GTLE KVDA E+AAR + +  L GN  G GRELF   R A  +
Sbjct: 543 PLGRVRDGDIIRLDAEAGTLEAKVDATEWAARSQDSSDLSGNQHGMGRELFSLFRNAVGT 602

Query: 593 AEQGASAF 600
           AE+G + F
Sbjct: 603 AEEGGATF 610


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: 1134
Number of extensions: 52
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: 623
Length adjustment: 37
Effective length of query: 571
Effective length of database: 586
Effective search space:   334606
Effective search space used:   334606
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 HSERO_RS05520 HSERO_RS05520 (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.27190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.7e-305  999.3   2.1   3.1e-305  999.1   2.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05520  HSERO_RS05520 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05520  HSERO_RS05520 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  999.1   2.1  3.1e-305  3.1e-305       2     600 ..       5     610 ..       4     611 .. 0.98

  Alignments for each domain:
  == domain 1  score: 999.1 bits;  conditional E-value: 3.1e-305
                                  TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlai 69 
                                                + la++t+ri ers+++r +yle++++a++kg +r++l+c+nlahg+aa + ++k++lk++k + lai
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520   5 ATLASVTQRIAERSRPYRTAYLERLEAARRKGAQRGALACTNLAHGFAAFPANDKLKLKEDKAPSLAI 72 
                                                56899*************************************************************** PP

                                  TIGR01196  70 itayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstai 137
                                                ++ayndmlsahqpf+++p++ik+a++ea+avaq agG pamcdGvtqG++Gmelsl+srd ia++tai
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520  73 VSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQAGMELSLFSRDAIAMATAI 140
                                                ******************************************************************** PP

                                  TIGR01196 138 glshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdree 205
                                                +lshnmfd+al+lGvcdkivpGlli+al fGhlpavfvpaGpm+sG++n++k+k+rql++ Gk++r e
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 141 ALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTSGMSNSDKVKIRQLYTAGKIGRAE 208
                                                ******************************************************************** PP

                                  TIGR01196 206 llksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltaknge 273
                                                ll++e++syh++GtctfyGtansnqml+e mGlhlpga+f+ pntplrdalt++aak++a++t  + +
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 209 LLEAESKSYHGAGTCTFYGTANSNQMLMEAMGLHLPGAAFITPNTPLRDALTAAAAKQAAKITDLGTQ 276
                                                ******************************************************************** PP

                                  TIGR01196 274 vlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGka 341
                                                ++p++++ideksivna+v+l+atGGstnhtlhlvaia+aaGi+++wdd+++ls +vpl++++ypnG+a
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 277 YTPVGRMIDEKSIVNAIVALHATGGSTNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTA 344
                                                ******************************************************************** PP

                                  TIGR01196 342 dvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfl....edgk...leyreaaeksld 402
                                                dvnhf+aaGG +f++rel+++Gl+h+dv+t++g+Glr+++kep+l    e+g+   +++++a+ +s d
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 345 DVNHFHAAGGTGFVLRELIDAGLMHDDVTTILGQGLRQHCKEPMLaaegENGRpgiVTWHDAPAQSGD 412
                                                ********************************************94433233244499********** PP

                                  TIGR01196 403 edilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlv 470
                                                e +l +v kpf+a+GGlkll+GnlGravik+savk+e+rv+eapa+vf++q+ ++aafkag+l+rd+v
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 413 EGVLGTVAKPFAADGGLKLLQGNLGRAVIKISAVKPEHRVVEAPAVVFHSQEAFMAAFKAGQLDRDFV 480
                                                ******************************************************************** PP

                                  TIGR01196 471 avvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakir 538
                                                av+ fqGp+anGmpelh lt++lG+lqd+g  valvtdGr+sGasGkvpaaihvtpe l gG+l ++r
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 481 AVITFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGGPLGRVR 548
                                                ******************************************************************** PP

                                  TIGR01196 539 dGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                                dGd+irlda +g le  vd +e++ar+ ++ dl+ n+ G+Grelf+ +r++v++aeeG++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS05520 549 DGDIIRLDAEAGTLEAKVDATEWAARSQDSSDLSGNQHGMGRELFSLFRNAVGTAEEGGATF 610
                                                ***********************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (623 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.74
//
[ok]

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

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Protein sequences (fasta format)
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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