Alignments for a candidate for icd in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Pseudomonas benzenivorans DSM 8628

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_090438861.1 BLS63_RS01575 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::Q02NB5
         (418 letters)



>NCBI__GCF_900100495.1:WP_090438861.1
          Length = 418

 Score =  776 bits (2004), Expect = 0.0
 Identities = 379/418 (90%), Positives = 401/418 (95%)

Query: 1   MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60
           MGYQKIQVPATGDKITVNADMSL+VP NPIIPFIEGDGIGVDISPVMIKVVDAAVEKAY 
Sbjct: 1   MGYQKIQVPATGDKITVNADMSLNVPNNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYG 60

Query: 61  GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120
           GERKI+WMEVYAGEKATQVYDQDTWLPQETLDAV+DYVVSIKGPLTTPVGGGIRSLNVAL
Sbjct: 61  GERKISWMEVYAGEKATQVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVAL 120

Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180
           RQQLDLYVC RPVRWFEGVPSPVKKPGDVDM IFRENSEDIYAG+EWKAGSPEA KVIKF
Sbjct: 121 RQQLDLYVCLRPVRWFEGVPSPVKKPGDVDMTIFRENSEDIYAGIEWKAGSPEANKVIKF 180

Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240
           L EEMGV KIRF ++CGIG+KPVS+EGTKRL RKALQY VDNDR S+T+VHKGNIMKFTE
Sbjct: 181 LKEEMGVTKIRFDQDCGIGVKPVSKEGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTE 240

Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300
           GAFK+W YE+A +EFGA LLDGGPWMQFKNPKTGKN++VKD IADAMLQQILLRPAEYDV
Sbjct: 241 GAFKEWAYEIAAEEFGATLLDGGPWMQFKNPKTGKNIIVKDAIADAMLQQILLRPAEYDV 300

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

Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           SAEMMLRHMGWTEAADLIIKGTNGAI+AKTVTYDFERLM+GA LLSCS+FGDAMI+ M
Sbjct: 361 SAEMMLRHMGWTEAADLIIKGTNGAISAKTVTYDFERLMEGAKLLSCSQFGDAMISHM 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: 791
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 WP_090438861.1 BLS63_RS01575 (NADP-dependent 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.26606.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-224  731.2   0.8   1.9e-224  731.0   0.8    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090438861.1  BLS63_RS01575 NADP-dependent iso


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090438861.1  BLS63_RS01575 NADP-dependent isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.0   0.8  1.9e-224  1.9e-224       2     416 ..       3     418 .]       2     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 731.0 bits;  conditional E-value: 1.9e-224
                                 TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevy 69 
                                               ++k+++p++G+kit++++  l+vpnnpiip+ieGdGiGvdi p +ikv+daavekay+ge+ki+w+evy
  lcl|NCBI__GCF_900100495.1:WP_090438861.1   3 YQKIQVPATGDKITVNADmSLNVPNNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYGGERKISWMEVY 71 
                                               78*************875279************************************************ PP

                                 TIGR00183  70 aGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvp 138
                                               aGeka+++y+++++lp++tlda+k+y v+ikGplttpvGgGirslnvalrq+ldlyvclrpvr+++gvp
  lcl|NCBI__GCF_900100495.1:WP_090438861.1  72 AGEKATQVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRWFEGVP 140
                                               ********************************************************************* PP

                                 TIGR00183 139 spvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtk 207
                                               spvk+p +vd+ ifren+ediyaGiew++gs ea+k+ikflk+e++v+kir+ +d+GiG+kp+s+egtk
  lcl|NCBI__GCF_900100495.1:WP_090438861.1 141 SPVKKPGDVDMTIFRENSEDIYAGIEWKAGSPEANKVIKFLKEEMGVTKIRFDQDCGIGVKPVSKEGTK 209
                                               ********************************************************************* PP

                                 TIGR00183 208 rlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkiv 276
                                               rl rka++y ++nd++s+t+vhkGnimkfteGafk+w ye+a +efg+++++ ++w + knp++Gk+i+
  lcl|NCBI__GCF_900100495.1:WP_090438861.1 210 RLARKALQYVVDNDRDSLTIVHKGNIMKFTEGAFKEWAYEIAAEEFGATLLDGGPWMQFKNPKTGKNII 278
                                               ********************************************************************* PP

                                 TIGR00183 277 vkdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapky 345
                                               vkd iada+lqqil+rp+eydviat+nlnGdylsdalaa vGG+GiapGan++d+va+feathGtapky
  lcl|NCBI__GCF_900100495.1:WP_090438861.1 279 VKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKY 347
                                               ********************************************************************* PP

                                 TIGR00183 346 aGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaive 414
                                               aG+d+vnpgs+ils++++l+++Gw+eaadli+k+ + ai++k+vtyd++rlm+gak + cs+f++a+++
  lcl|NCBI__GCF_900100495.1:WP_090438861.1 348 AGKDQVNPGSLILSAEMMLRHMGWTEAADLIIKGTNGAISAKTVTYDFERLMEGAKLLSCSQFGDAMIS 416
                                               ********************************************************************* PP

                                 TIGR00183 415 nl 416
                                               ++
  lcl|NCBI__GCF_900100495.1:WP_090438861.1 417 HM 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: 9.16
//
[ok]

This GapMind analysis is from Sep 24 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