Alignments for a candidate for icd in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Pseudomonas simiae WCS417

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate GFF3228 PS417_16525 isocitrate dehydrogenase

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__WCS417:GFF3228
          Length = 418

 Score =  754 bits (1948), Expect = 0.0
 Identities = 374/418 (89%), Positives = 394/418 (94%)

Query: 1   MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60
           MGY+KIQVPA GDKITVNAD SL+VP  PIIP+IEGDGIGVDISPVMIKVVDAAVEKAY 
Sbjct: 1   MGYKKIQVPAVGDKITVNADHSLNVPDQPIIPYIEGDGIGVDISPVMIKVVDAAVEKAYG 60

Query: 61  GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120
           G+RKI+WMEVYAGEKATQVYDQDTWLPQETLDAV+DYVVSIKGPLTTPVGGGIRSLNVAL
Sbjct: 61  GKRKISWMEVYAGEKATQVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVAL 120

Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180
           RQQLDLYVC RPVRWFEGVPSPVKKPGDVDM IFRENSEDIYAG+EWKAGS EA KVIKF
Sbjct: 121 RQQLDLYVCLRPVRWFEGVPSPVKKPGDVDMTIFRENSEDIYAGIEWKAGSAEAIKVIKF 180

Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240
           L EEMGV KIRF ++CGIGIKPVS EGTKRL RKALQY VDNDR S+T+VHKGNIMKFTE
Sbjct: 181 LKEEMGVTKIRFDQDCGIGIKPVSLEGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTE 240

Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300
           GAFK+W YEVA +EFGA LLDGGPWMQFKNPKTGKNVVVKD IADAMLQQILLRPAEYDV
Sbjct: 241 GAFKEWAYEVAAEEFGATLLDGGPWMQFKNPKTGKNVVVKDAIADAMLQQILLRPAEYDV 300

Query: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL 360
           IATLNLNGDYLSDALAAEVGGIGIAPGANLSD+VAMFEATHGTAPKYAG+D+VNPGSLIL
Sbjct: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGKDQVNPGSLIL 360

Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           SAEMMLRHMGWTEAADLIIKGTNGAI+AKTVTYDFERLMDGA L+S S FGDA+I+ M
Sbjct: 361 SAEMMLRHMGWTEAADLIIKGTNGAISAKTVTYDFERLMDGAKLVSSSGFGDALISHM 418


Lambda     K      H
   0.317    0.135    0.397 

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: 767
Number of extensions: 20
Number of successful extensions: 1
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate GFF3228 PS417_16525 (isocitrate dehydrogenase)
to HMM TIGR00183 (icd: isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# 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/TIGR00183.hmm
# target sequence database:        /tmp/gapView.26977.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00183  [M=417]
Accession:   TIGR00183
Description: prok_nadp_idh: isocitrate dehydrogenase, NADP-dependent
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-221  721.5   1.1   1.6e-221  721.3   1.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF3228  PS417_16525 isocitrate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3228  PS417_16525 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.3   1.1  1.6e-221  1.6e-221       2     416 ..       3     418 .]       2     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 721.3 bits;  conditional E-value: 1.6e-221
                           TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekay 75 
                                         ++k+++p++G+kit++++  l+vp++piipyieGdGiGvdi p +ikv+daavekay+g++ki+w+evyaGeka+
  lcl|FitnessBrowser__WCS417:GFF3228   3 YKKIQVPAVGDKITVNADhSLNVPDQPIIPYIEGDGIGVDISPVMIKVVDAAVEKAYGGKRKISWMEVYAGEKAT 77 
                                         78*************865279****************************************************** PP

                           TIGR00183  76 elygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlv 150
                                         ++y+++++lp++tlda+k+y v+ikGplttpvGgGirslnvalrq+ldlyvclrpvr+++gvpspvk+p +vd+ 
  lcl|FitnessBrowser__WCS417:GFF3228  78 QVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRWFEGVPSPVKKPGDVDMT 152
                                         *************************************************************************** PP

                           TIGR00183 151 ifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksv 225
                                         ifren+ediyaGiew++gs+ea k+ikflk+e++v+kir+ +d+GiGikp+s egtkrl rka++y ++nd++s+
  lcl|FitnessBrowser__WCS417:GFF3228 153 IFRENSEDIYAGIEWKAGSAEAIKVIKFLKEEMGVTKIRFDQDCGIGIKPVSLEGTKRLARKALQYVVDNDRDSL 227
                                         *************************************************************************** PP

                           TIGR00183 226 tlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydvia 300
                                         t+vhkGnimkfteGafk+w ye+a +efg+++++ ++w + knp++Gk++vvkd iada+lqqil+rp+eydvia
  lcl|FitnessBrowser__WCS417:GFF3228 228 TIVHKGNIMKFTEGAFKEWAYEVAAEEFGATLLDGGPWMQFKNPKTGKNVVVKDAIADAMLQQILLRPAEYDVIA 302
                                         *************************************************************************** PP

                           TIGR00183 301 tmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadl 375
                                         t+nlnGdylsdalaa vGG+GiapGan++d+va+feathGtapkyaG+d+vnpgs+ils++++l+++Gw+eaadl
  lcl|FitnessBrowser__WCS417:GFF3228 303 TLNLNGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGKDQVNPGSLILSAEMMLRHMGWTEAADL 377
                                         *************************************************************************** PP

                           TIGR00183 376 ivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                         i+k+ + ai++k+vtyd++rlmdgak v +s f++a+++++
  lcl|FitnessBrowser__WCS417:GFF3228 378 IIKGTNGAISAKTVTYDFERLMDGAKLVSSSGFGDALISHM 418
                                         ***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (418 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: 10.50
//
[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