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.2110357.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.82
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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