Alignments for a candidate for edd in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Paraburkholderia bryophila 376MFSha3.1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate H281DRAFT_04278 H281DRAFT_04278 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Burk376:H281DRAFT_04278
          Length = 641

 Score =  759 bits (1960), Expect = 0.0
 Identities = 376/601 (62%), Positives = 470/601 (78%), Gaps = 2/601 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           H ++L+VT+R+V RS+ TREAYLA I  A    P RG L CAN AHG AG    DK  ++
Sbjct: 5   HSQLLKVTQRVVERSKPTREAYLARIHEAQGRFPARGALSCANLAHGFAGLEGNDKLVIK 64

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
            +   NV IVSSYN+MLSAH PY+++P+ IK+A RE G V QFAGG PAMCDG+TQG AG
Sbjct: 65  QIREPNVGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGITQGNAG 124

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           MELSL SREVIA+STAVAL+HNMFDAAL LGICDKIVPGL++GAL+FGHLPTIFVP GPM
Sbjct: 125 MELSLFSREVIAMSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPM 184

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            SG+SN +KA  RQ++A G+  R+ LLE+E  +YH  GTCTFYGTAN+NQ+LME+MGLHL
Sbjct: 185 TSGLSNDDKAKTRQQFATGQCGRDALLEAEAAAYHGHGTCTFYGTANSNQMLMEIMGLHL 244

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           PG++FV+P+TPLRDALT +AA++V  LT + G++ PIG ++DE+++VN IVAL ATGGST
Sbjct: 245 PGSAFVHPHTPLRDALTAQAARRVLDLTVERGHYMPIGHVIDEKAIVNGIVALLATGGST 304

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHTLH+ AIA+AAGI + W D   LS+ VP L+ +YPNGKAD+NHF AAGG+AFL+R LL
Sbjct: 305 NHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAGGVAFLVRNLL 364

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421
           E GLLHEDVNTVAG+GL  YT+EP L +GKL W  G   S D  +LR +   F  +GGLR
Sbjct: 365 EGGLLHEDVNTVAGKGLHHYTEEPKLLDGKLQWVPGVQASEDTAVLRGIKEPFQADGGLR 424

Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481
           +M+G LGRGV+K+SAVA QH+ V+APA+VF  Q+ + +AF  GEL++DF+AV+RFQG R+
Sbjct: 425 LMQGKLGRGVIKISAVAQQHRKVKAPAIVFDSQEAVQEAFDNGELKRDFIAVVRFQGARA 484

Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541
           NGMPELH++TP LGVLQD+GF VALVTDGRMSGASGK+PA IH+SPEA + G + +VR G
Sbjct: 485 NGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRSG 544

Query: 542 DIIRVDGVKGTLELKVDADEFAAREPAKGL--LGNNVGSGRELFGFMRMAFSSAEQGASA 599
           D++ +D   G L++++D  E+AAR  A  L    N VG GRELFG  R A + AEQGAS 
Sbjct: 545 DMLVIDAEAGVLDIEIDPAEWAARPNAVPLHQAENEVGFGRELFGVFRAAAAPAEQGASV 604

Query: 600 F 600
           F
Sbjct: 605 F 605


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: 1192
Number of extensions: 49
Number of successful extensions: 2
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: 641
Length adjustment: 37
Effective length of query: 571
Effective length of database: 604
Effective search space:   344884
Effective search space used:   344884
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: 54 (25.4 bits)

Align candidate H281DRAFT_04278 H281DRAFT_04278 (6-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.25666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.7e-299  980.2   0.8   1.9e-299  980.0   0.8    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04278  H281DRAFT_04278 6-phosphoglucona


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04278  H281DRAFT_04278 6-phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  980.0   0.8  1.9e-299  1.9e-299       1     600 [.       5     605 ..       5     606 .. 0.99

  Alignments for each domain:
  == domain 1  score: 980.0 bits;  conditional E-value: 1.9e-299
                                    TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrkn 66 
                                                  hs+l+++t+r++ersk+tre+yl++i++a+ + + r++l+c+nlahg+a l+ ++k+ +k+ +++n
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278   5 HSQLLKVTQRVVERSKPTREAYLARIHEAQGRFPARGALSCANLAHGFAGLEGNDKLVIKQIREPN 70 
                                                  89**************************************************************** PP

                                    TIGR01196  67 laiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvia 132
                                                  ++i+++yn+mlsah p+k+ypd+ik+a++e+++vaq agGvpamcdG+tqG++Gmelsl+sr+via
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278  71 VGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGITQGNAGMELSLFSREVIA 136
                                                  ****************************************************************** PP

                                    TIGR01196 133 lstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfae 198
                                                  +sta++l+hnmfd+al+lG+cdkivpGlli+al fGhlp++fvpaGpm+sGl+n++kak+rq+fa 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 137 MSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPMTSGLSNDDKAKTRQQFAT 202
                                                  ****************************************************************** PP

                                    TIGR01196 199 GkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrl 264
                                                  G+ +r++ll++e+a+yh+ GtctfyGtansnqml+e+mGlhlpg++fv+p+tplrdalt++aa+r+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 203 GQCGRDALLEAEAAAYHGHGTCTFYGTANSNQMLMEIMGLHLPGSAFVHPHTPLRDALTAQAARRV 268
                                                  ****************************************************************** PP

                                    TIGR01196 265 arltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvp 330
                                                    lt + g+++p++++idek+ivn++v+llatGGstnhtlhlvaiaraaGi+++wdd++ ls+ vp
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 269 LDLTVERGHYMPIGHVIDEKAIVNGIVALLATGGSTNHTLHLVAIARAAGIVIDWDDFDTLSQAVP 334
                                                  ****************************************************************** PP

                                    TIGR01196 331 llarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyrea 396
                                                  lla++ypnGkadvnhf+aaGG++fl+r+ll+ Gllhedv+tvagkGl++yt+ep+l dgkl++ ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 335 LLAKIYPNGKADVNHFHAAGGVAFLVRNLLEGGLLHEDVNTVAGKGLHHYTEEPKLLDGKLQWVPG 400
                                                  ****************************************************************** PP

                                    TIGR01196 397 aeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafka 462
                                                  +++s d+++lr +++pf+a+GGl+l++G lGr+vik+sav++++r+++apaivf++q+ +++af++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 401 VQASEDTAVLRGIKEPFQADGGLRLMQGKLGRGVIKISAVAQQHRKVKAPAIVFDSQEAVQEAFDN 466
                                                  ****************************************************************** PP

                                    TIGR01196 463 gelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpea 528
                                                  gel+rd++avvrfqG +anGmpelh+lt+ lGvlqd+gf valvtdGr+sGasGkvpa ih++pea
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 467 GELKRDFIAVVRFQGARANGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEA 532
                                                  ****************************************************************** PP

                                    TIGR01196 529 legGalakirdGdlirldavngelevlvddaelkareleeld.lednelGlGrelfaalrekvssa 593
                                                  l +G++ k+r Gd++ +da +g l++ +d ae++ar  + +    +ne+G Grelf  +r +++ a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 533 LLQGPIGKVRSGDMLVIDAEAGVLDIEIDPAEWAARPNAVPLhQAENEVGFGRELFGVFRAAAAPA 598
                                                  ************************************877654277899****************** PP

                                    TIGR01196 594 eeGassl 600
                                                  e+Gas++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04278 599 EQGASVF 605
                                                  ****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (641 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.69
//
[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:

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