Alignments for a candidate for edd in Alicycliphilus denitrificans K601

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Alicycliphilus denitrificans K601

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_013722484.1 ALIDE2_RS14965 phosphogluconate dehydratase

Query= SwissProt::P21909
         (607 letters)



>NCBI__GCF_000204645.1:WP_013722484.1
          Length = 605

 Score =  674 bits (1739), Expect = 0.0
 Identities = 344/601 (57%), Positives = 433/601 (72%), Gaps = 10/601 (1%)

Query: 5   HSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNG-DKPALR 63
           H TV  VT R+ +RS  TR AYL  ++    +      L C+N+AH FAAM G DK  + 
Sbjct: 4   HETVHTVTERIRQRSAATRDAYLQQLESHARRDRGAARLGCANVAHAFAAMPGSDKLRVV 63

Query: 64  DFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQPG 123
                NIG+VTSYNDMLSAH P   YP  +K  AR  GAT QVAGGVPAMCDGVTQG PG
Sbjct: 64  AQKAPNIGIVTSYNDMLSAHAPLASYPGLIKDEARRCGATAQVAGGVPAMCDGVTQGTPG 123

Query: 124 MEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSGPM 183
           ME SLFSRDVIA+AT+V+LSH +F+ A +LG+CDKIVPGLL+GAL+FG+LPT+ VP+GPM
Sbjct: 124 MELSLFSRDVIAMATAVALSHDVFDAALMLGVCDKIVPGLLVGALQFGYLPTVFVPAGPM 183

Query: 184 TTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLHM 243
           T+G+ N  K ++R+  AQG +G+ ELL  E A YH+ GTCTFYGTAN+NQM++E +GLH+
Sbjct: 184 TSGLSNSAKAKVREQAAQGLVGRGELLQAEMAAYHSPGTCTFYGTANSNQMLLEAMGLHV 243

Query: 244 PGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGST 303
           PG+AFV PG  LR+ LTR A   V  LG  G    P+G+++DE++IVNA+V LLATGGST
Sbjct: 244 PGTAFVNPGHALREELTREAARTV--LGSAGAPCPPIGRVVDERAIVNAMVALLATGGST 301

Query: 304 NHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKELL 363
           NH +H  A+ARAAG++++W+DF  LS  VPL+AR+YPNG  D+N FQ AGG  YVI+ELL
Sbjct: 302 NHLIHWVAVARAAGIVIDWDDFSALSAAVPLLARVYPNGSADVNRFQAAGGPGYVIRELL 361

Query: 364 SANLLNRDVTTIAKGGIEEYAKAPALNDAGE-LVWKPAGEPGDDTILRPVSNPFAKDGGL 422
            A L++ DV T+  GGI EY + P   DAG+ L W   G   DD++LRP ++PF+  GGL
Sbjct: 362 DAGLMHEDVLTVRPGGIREYTRVPE-GDAGQRLRWADVGASRDDSVLRPAADPFSATGGL 420

Query: 423 RLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGPR 482
           +LL GNLGR++ K SAV      +EAP RVF+ Q ++ +AF+AGEL +DV+ VVR+QGPR
Sbjct: 421 KLLSGNLGRSVIKVSAVPRDHHVVEAPARVFASQGELLQAFQAGELERDVVCVVRWQGPR 480

Query: 483 ANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLRD 542
           ANGMPELHKLTP L VLQ  G+KVALVTDGRMSGA+GKVP A+H SPEA  GG + ++RD
Sbjct: 481 ANGMPELHKLTPPLAVLQGKGHKVALVTDGRMSGASGKVPAAIHASPEAHAGGPLARVRD 540

Query: 543 GDIVRISVEEGKLEALVPADEWNAR-PHAEKPAFRP----GTGRELFDIFRQNAAKAEDG 597
           GD +R+    G L+ L+ A EW AR P A  P        G GRELF  FR+NA  AE+G
Sbjct: 541 GDPIRLDAVAGTLDVLIDAAEWQARQPAAMPPGLHEDNAHGWGRELFAGFRRNALSAEEG 600

Query: 598 A 598
           A
Sbjct: 601 A 601


Lambda     K      H
   0.318    0.136    0.403 

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: 1169
Number of extensions: 40
Number of successful extensions: 4
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: 607
Length of database: 605
Length adjustment: 37
Effective length of query: 570
Effective length of database: 568
Effective search space:   323760
Effective search space used:   323760
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_013722484.1 ALIDE2_RS14965 (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.108152.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-281  921.0   0.0   1.6e-281  920.8   0.0    1.0  1  NCBI__GCF_000204645.1:WP_013722484.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204645.1:WP_013722484.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  920.8   0.0  1.6e-281  1.6e-281       2     599 ..       5     603 ..       4     605 .] 0.98

  Alignments for each domain:
  == domain 1  score: 920.8 bits;  conditional E-value: 1.6e-281
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 
                                             +  +teri +rs++tr++yl++++s +++ +  ++lgc+n+ah++aa++ s+k+ +  +k +n++i+t+yn
  NCBI__GCF_000204645.1:WP_013722484.1   5 ETVHTVTERIRQRSAATRDAYLQQLESHARRDRGAARLGCANVAHAFAAMPGSDKLRVVAQKAPNIGIVTSYN 77 
                                           56899******************************************************************** PP

                             TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147
                                           dmlsah p+++yp+lik+++++ +a+aqvagGvpamcdGvtqG +Gmelsl+srdvia++ta++lsh++fd+a
  NCBI__GCF_000204645.1:WP_013722484.1  78 DMLSAHAPLASYPGLIKDEARRCGATAQVAGGVPAMCDGVTQGTPGMELSLFSRDVIAMATAVALSHDVFDAA 150
                                           ************************************************************************* PP

                             TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                           l+lGvcdkivpGll++al fG lp+vfvpaGpm+sGl+n+ kakvr++ a+G v+r ell++ema+yh+pGtc
  NCBI__GCF_000204645.1:WP_013722484.1 151 LMLGVCDKIVPGLLVGALQFGYLPTVFVPAGPMTSGLSNSAKAKVREQAAQGLVGRGELLQAEMAAYHSPGTC 223
                                           ************************************************************************* PP

                             TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293
                                           tfyGtansnqml+e mGlh+pg++fvnp   lr++ltreaa+ +    + ++ + p+++++de++ivna+v+l
  NCBI__GCF_000204645.1:WP_013722484.1 224 TFYGTANSNQMLLEAMGLHVPGTAFVNPGHALREELTREAARTVLG--SAGAPCPPIGRVVDERAIVNAMVAL 294
                                           *******************************************998..669999******************* PP

                             TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366
                                           latGGstnh +h va+araaGi+++wdd+s+ls  vpllarvypnG+advn f+aaGG +++irell++Gl+h
  NCBI__GCF_000204645.1:WP_013722484.1 295 LATGGSTNHLIHWVAVARAAGIVIDWDDFSALSAAVPLLARVYPNGSADVNRFQAAGGPGYVIRELLDAGLMH 367
                                           ************************************************************************* PP

                             TIGR01196 367 edvetvagkGlrrytkepfledgk.leyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438
                                           edv tv   G+r+yt+ p  + g+ l++   + +s d+++lr++ +pfsa+GGlkll+GnlGr+vikvsav  
  NCBI__GCF_000204645.1:WP_013722484.1 368 EDVLTVRPGGIREYTRVPEGDAGQrLRWA-DVGASRDDSVLRPAADPFSATGGLKLLSGNLGRSVIKVSAVPR 439
                                           *******************9997616665.5789*************************************** PP

                             TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511
                                           +++v+eapa+vf +q ell+af+agelerd+v+vvr+qGp+anGmpelhklt++l vlq +g+kvalvtdGr+
  NCBI__GCF_000204645.1:WP_013722484.1 440 DHHVVEAPARVFASQGELLQAFQAGELERDVVCVVRWQGPRANGMPELHKLTPPLAVLQGKGHKVALVTDGRM 512
                                           ************************************************************************* PP

                             TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeld...lednelGlGre 581
                                           sGasGkvpaaih +pea +gG+la++rdGd irldav+g l+vl+d ae++ar+++ +     edn  G Gre
  NCBI__GCF_000204645.1:WP_013722484.1 513 SGASGKVPAAIHASPEAHAGGPLARVRDGDPIRLDAVAGTLDVLIDAAEWQARQPAAMPpglHEDNAHGWGRE 585
                                           ******************************************************9998745457999****** PP

                             TIGR01196 582 lfaalrekvssaeeGass 599
                                           lfa +r+++ saeeGa++
  NCBI__GCF_000204645.1:WP_013722484.1 586 LFAGFRRNALSAEEGACT 603
                                           ****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (605 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.23
//
[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