Alignments for a candidate for edd in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas litoralis 2SM5

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_090272172.1 BLU11_RS04110 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_900105005.1:WP_090272172.1
          Length = 612

 Score =  774 bits (1998), Expect = 0.0
 Identities = 387/604 (64%), Positives = 467/604 (77%), Gaps = 2/604 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRV+EVTERLV RSR +R AYL  +  AA+    R  L C+NFAHG+AGC + DK  L
Sbjct: 1   MHPRVIEVTERLVERSRLSRAAYLQQMAEAAARPRGRRDLSCSNFAHGMAGCSAVDKDRL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RM++  N+ +V++YNDMLSAHQPYE +P QI++ALR  G+ GQ AGG PAMCDGVTQGE 
Sbjct: 61  RMVDEVNIGMVTAYNDMLSAHQPYETYPAQIREALRAFGATGQVAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIA+ TA+ALSHNMFDAAL LGICDKIVPGL+MGALRFGHLP +FVP GP
Sbjct: 121 GMELSLVSRDVIAMGTAIALSHNMFDAALCLGICDKIVPGLLMGALRFGHLPILFVPAGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSG+ N EKA VRQR+AEG ATREELL++E K+YH+PGTCTFYGTANTNQ+L+E MGL 
Sbjct: 181 MPSGLPNSEKALVRQRFAEGLATREELLDAESKAYHAPGTCTFYGTANTNQMLLEAMGLQ 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASF+NP TPLRDALT   A+Q  RL +       +  I+DER+LVN++V L ATGGS
Sbjct: 241 LPGASFINPGTPLRDALTVHVAEQAARLARAGEG--SLASILDERALVNALVVLLATGGS 298

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN TLH+ AI Q AG+QL W DMA+LSEVVPTL+ +YPNG+AD+NHFQAAGG AFL  +L
Sbjct: 299 TNLTLHLIAIGQCAGLQLNWSDMAELSEVVPTLARIYPNGQADVNHFQAAGGSAFLFAQL 358

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LE GLLH DVNT+AG GL RYT EP L +G+L WRDGP  SLD++ILR +   F  +GGL
Sbjct: 359 LEGGLLHADVNTIAGPGLQRYTHEPTLVDGRLAWRDGPAASLDDSILRSLRAPFKVDGGL 418

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R++EG+LGR V+KVSAV  +H  V AP   F  Q+    AF+  E + D + V+RFQGP 
Sbjct: 419 RLVEGDLGRSVIKVSAVKPEHWQVSAPCRTFVTQEAFVTAFQNNEFDSDVIVVIRFQGPA 478

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELHK+TP+LGVLQDRG +VALVTDGRMSGASGK+PA IH+SPEA  GG +A +RD
Sbjct: 479 ANGMPELHKLTPYLGVLQDRGLRVALVTDGRMSGASGKVPAVIHMSPEAHSGGPIACLRD 538

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDI+ +D  +GTL +++D  E+ +R PA        G GRELF F R A S AEQGAS F
Sbjct: 539 GDILDLDADRGTLLVRMDEAEWQSRTPAVHPQPVRRGWGRELFAFARTAASPAEQGASCF 598

Query: 601 TSAL 604
           T +L
Sbjct: 599 TESL 602


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: 1144
Number of extensions: 41
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: 612
Length adjustment: 37
Effective length of query: 571
Effective length of database: 575
Effective search space:   328325
Effective search space used:   328325
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_090272172.1 BLU11_RS04110 (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.2092211.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-281  919.4   0.0   4.6e-281  919.2   0.0    1.0  1  NCBI__GCF_900105005.1:WP_090272172.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090272172.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  919.2   0.0  4.6e-281  4.6e-281       1     601 []       2     599 ..       2     599 .. 0.99

  Alignments for each domain:
  == domain 1  score: 919.2 bits;  conditional E-value: 4.6e-281
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h+r+ e+ter++ers+  r +yl+++ +a+ +++ r+ l+c+n+ahg+a +s  +k  l+   + n++++tay
  NCBI__GCF_900105005.1:WP_090272172.1   2 HPRVIEVTERLVERSRLSRAAYLQQMAEAAARPRGRRDLSCSNFAHGMAGCSAVDKDRLRMVDEVNIGMVTAY 74 
                                           79*********************************************************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqp+++yp++i++al+  +a++qvagGvpamcdGvtqGe+Gmelsl+srdvia+ tai+lshnmfd+
  NCBI__GCF_900105005.1:WP_090272172.1  75 NDMLSAHQPYETYPAQIREALRAFGATGQVAGGVPAMCDGVTQGEPGMELSLVSRDVIAMGTAIALSHNMFDA 147
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           al+lG+cdkivpGll++al fGhlp +fvpaGpm+sGl+n+eka vrq faeG ++reell++e+++yhapGt
  NCBI__GCF_900105005.1:WP_090272172.1 148 ALCLGICDKIVPGLLMGALRFGHLPILFVPAGPMPSGLPNSEKALVRQRFAEGLATREELLDAESKAYHAPGT 220
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtan+nqml+e mGl+lpgasf+np tplrdalt + a+++arl  ++ge   la ++de+++vnalv 
  NCBI__GCF_900105005.1:WP_090272172.1 221 CTFYGTANTNQMLLEAMGLQLPGASFINPGTPLRDALTVHVAEQAARLA-RAGE-GSLASILDERALVNALVV 291
                                           ***********************************************76.5555.4699************** PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           llatGGstn tlhl+ai ++aG++lnw d+ els++vp+lar+ypnG+advnhf+aaGG +fl ++ll+ Gll
  NCBI__GCF_900105005.1:WP_090272172.1 292 LLATGGSTNLTLHLIAIGQCAGLQLNWSDMAELSEVVPTLARIYPNGQADVNHFQAAGGSAFLFAQLLEGGLL 364
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438
                                           h dv+t+ag Gl+ryt+ep l dg+l +r+++ +sld++ilr++  pf+ +GGl+l++G+lGr+vikvsavk+
  NCBI__GCF_900105005.1:WP_090272172.1 365 HADVNTIAGPGLQRYTHEPTLVDGRLAWRDGPAASLDDSILRSLRAPFKVDGGLRLVEGDLGRSVIKVSAVKP 437
                                           ************************************************************************* PP

                             TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511
                                           e+  + ap++ f +q+ +++af+++e++ d+++v+rfqGp anGmpelhklt+ lGvlqdrg +valvtdGr+
  NCBI__GCF_900105005.1:WP_090272172.1 438 EHWQVSAPCRTFVTQEAFVTAFQNNEFDSDVIVVIRFQGPAANGMPELHKLTPYLGVLQDRGLRVALVTDGRM 510
                                           ************************************************************************* PP

                             TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfa 584
                                           sGasGkvpa ih++pea +gG++a +rdGd++ lda  g l v +d+ae+++r++  ++++  + G Grelfa
  NCBI__GCF_900105005.1:WP_090272172.1 511 SGASGKVPAVIHMSPEAHSGGPIACLRDGDILDLDADRGTLLVRMDEAEWQSRTP-AVHPQPVRRGWGRELFA 582
                                           *****************************************************95.678999*********** PP

                             TIGR01196 585 alrekvssaeeGasslt 601
                                           + r+++s ae+Gas++t
  NCBI__GCF_900105005.1:WP_090272172.1 583 FARTAASPAEQGASCFT 599
                                           ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (612 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 27.38
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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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 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