Alignments for a candidate for icd in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Pseudomonas fluorescens GW456-L13

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate PfGW456L13_2643 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643
          Length = 418

 Score =  761 bits (1964), Expect = 0.0
 Identities = 374/418 (89%), Positives = 396/418 (94%)

Query: 1   MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60
           MGY+KIQVPA GDKITVNAD SL+VP NPIIPFIEGDGIGVDISPVMIKVVDAAV+KAY 
Sbjct: 1   MGYKKIQVPAVGDKITVNADHSLNVPNNPIIPFIEGDGIGVDISPVMIKVVDAAVKKAYG 60

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

Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180
           RQQLDLYVC RPVRWFEGVPSPVKKPGDVDM IFRENSEDIYAG+EWKAG+PEA KVIKF
Sbjct: 121 RQQLDLYVCLRPVRWFEGVPSPVKKPGDVDMTIFRENSEDIYAGIEWKAGTPEATKVIKF 180

Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240
           L EEMGV KIRF ENCGIG+KPVS +GTKRL RKALQY VDNDR S+T+VHKGNIMKFTE
Sbjct: 181 LKEEMGVTKIRFDENCGIGVKPVSLQGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTE 240

Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300
           GAFK+W YEVA +EFGA LLDGGPWMQFKNPKTGKNV+VKD IADAMLQQILLRPAEYDV
Sbjct: 241 GAFKEWAYEVAAEEFGATLLDGGPWMQFKNPKTGKNVIVKDAIADAMLQQILLRPAEYDV 300

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

Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           SAEMMLRHMGWTEAADLIIKGTNGAI+AKTVTYDFERLM+GA L+S S FGDA+I+ M
Sbjct: 361 SAEMMLRHMGWTEAADLIIKGTNGAISAKTVTYDFERLMEGAKLVSSSGFGDALISHM 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: 772
Number of extensions: 19
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 PfGW456L13_2643 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
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.14336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.5e-221  721.4   0.9   1.7e-221  721.2   0.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643  Isocitrate dehydrogenase [NADP] 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643  Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.2   0.9  1.7e-221  1.7e-221       2     416 ..       3     418 .]       2     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 721.2 bits;  conditional E-value: 1.7e-221
                                               TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavek 55 
                                                             ++k+++p++G+kit++++  l+vpnnpiip+ieGdGiGvdi p +ikv+daav+k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643   3 YKKIQVPAVGDKITVNADhSLNVPNNPIIPFIEGDGIGVDISPVMIKVVDAAVKK 57 
                                                             78*************865279********************************** PP

                                               TIGR00183  56 aykgekkiawfevyaGekayelygeeeylpedtldaikeykvaikGplttpvGgG 110
                                                             ay+ge+ki+w+evyaGeka+++y+++++lp++tlda+k+y v+ikGplttpvGgG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643  58 AYGGERKISWMEVYAGEKATQVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGG 112
                                                             ******************************************************* PP

                                               TIGR00183 111 irslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifrentediyaGiew 165
                                                             irslnvalrq+ldlyvclrpvr+++gvpspvk+p +vd+ ifren+ediyaGiew
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 113 IRSLNVALRQQLDLYVCLRPVRWFEGVPSPVKKPGDVDMTIFRENSEDIYAGIEW 167
                                                             ******************************************************* PP

                                               TIGR00183 166 aegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaien 220
                                                             ++g+ ea k+ikflk+e++v+kir+ e++GiG+kp+s +gtkrl rka++y ++n
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 168 KAGTPEATKVIKFLKEEMGVTKIRFDENCGIGVKPVSLQGTKRLARKALQYVVDN 222
                                                             ******************************************************* PP

                                               TIGR00183 221 dkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkki 275
                                                             d++s+t+vhkGnimkfteGafk+w ye+a +efg+++++ ++w + knp++Gk++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 223 DRDSLTIVHKGNIMKFTEGAFKEWAYEVAAEEFGATLLDGGPWMQFKNPKTGKNV 277
                                                             ******************************************************* PP

                                               TIGR00183 276 vvkdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigd 330
                                                             +vkd iada+lqqil+rp+eydviat+nlnGdylsdalaa vGG+GiapGan++d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 278 IVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANLSD 332
                                                             ******************************************************* PP

                                               TIGR00183 331 evaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadlivkalekaia 385
                                                             +va+feathGtapkyaG+d+vnpgs+ils++++l+++Gw+eaadli+k+ + ai+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 333 TVAMFEATHGTAPKYAGKDQVNPGSLILSAEMMLRHMGWTEAADLIIKGTNGAIS 387
                                                             ******************************************************* PP

                                               TIGR00183 386 skevtydlarlmdgakevkcsefaeaivenl 416
                                                             +k+vtyd++rlm+gak v +s f++a+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 388 AKTVTYDFERLMEGAKLVSSSGFGDALISHM 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.15
//
[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