GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Pseudomonas fluorescens FW300-N2C3

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate AO356_22135 AO356_22135 isocitrate dehydrogenase

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_22135
          Length = 418

 Score =  760 bits (1962), Expect = 0.0
 Identities = 373/418 (89%), Positives = 397/418 (94%)

Query: 1   MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60
           MGYQKIQVPA GDKITVNAD SL+VP NPIIPFIEGDGIGVDISPVMIKVVDAAV+KAY 
Sbjct: 1   MGYQKIQVPAVGDKITVNADHSLNVPDNPIIPFIEGDGIGVDISPVMIKVVDAAVQKAYG 60

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

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

Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240
           L EEMGV KIRF E+CGIG+KPVS++GTKRL RKALQY VDNDR S+T+VHKGNIMKFTE
Sbjct: 181 LKEEMGVTKIRFDEDCGIGVKPVSKQGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTE 240

Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300
           GAFK+W YEVA +EFGA LLDGGPWMQFKNP+TGKNV+VKD IADAMLQQILLRPAEYDV
Sbjct: 241 GAFKEWAYEVAAEEFGATLLDGGPWMQFKNPRTGKNVIVKDAIADAMLQQILLRPAEYDV 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: 768
Number of extensions: 22
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 AO356_22135 AO356_22135 (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.10926.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   4.2e-222  723.3   0.6   4.9e-222  723.1   0.6    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135  AO356_22135 isocitrate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135  AO356_22135 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.1   0.6  4.9e-222  4.9e-222       2     416 ..       3     418 .]       2     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 723.1 bits;  conditional E-value: 4.9e-222
                                       TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekki 63 
                                                     ++k+++p++G+kit++++  l+vp+npiip+ieGdGiGvdi p +ikv+daav+kay+g++ki
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135   3 YQKIQVPAVGDKITVNADhSLNVPDNPIIPFIEGDGIGVDISPVMIKVVDAAVQKAYGGKRKI 65 
                                                     78*************865279****************************************** PP

                                       TIGR00183  64 awfevyaGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyv 126
                                                     +w+evyaGeka+++y+++++lp++tlda+k+y v+ikGplttpvGgGirslnvalrq+ldlyv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135  66 SWMEVYAGEKATQVYDQDTWLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYV 128
                                                     *************************************************************** PP

                                       TIGR00183 127 clrpvryykgvpspvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkir 189
                                                     clrpvr+++gvpspvk+p +vd+ ifren+ediyaGiew++gs ea k+ikflk+e++v+kir
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135 129 CLRPVRWFEGVPSPVKKPGDVDMTIFRENSEDIYAGIEWKAGSPEATKVIKFLKEEMGVTKIR 191
                                                     *************************************************************** PP

                                       TIGR00183 190 lpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakke 252
                                                     + ed+GiG+kp+s++gtkrl rka++y ++nd++s+t+vhkGnimkfteGafk+w ye+a +e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135 192 FDEDCGIGVKPVSKQGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTEGAFKEWAYEVAAEE 254
                                                     *************************************************************** PP

                                       TIGR00183 253 fgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmnlnGdylsdalaa 315
                                                     fg+++++ ++w + knp +Gk+++vkd iada+lqqil+rp+eydviat+nlnGdylsdalaa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135 255 FGATLLDGGPWMQFKNPRTGKNVIVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAA 317
                                                     *************************************************************** PP

                                       TIGR00183 316 lvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadlivk 378
                                                      vGG+GiapGan++d+va+feathGtapkyaG+d+vnpgs+ils++++l+++Gw+eaadli+k
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135 318 EVGGIGIAPGANLSDTVAMFEATHGTAPKYAGKDQVNPGSLILSAEMMLRHMGWTEAADLIIK 380
                                                     *************************************************************** PP

                                       TIGR00183 379 alekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                                     + + ai++k+vtyd++rlm+gak v +s f++a+++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22135 381 GTNGAISAKTVTYDFERLMEGAKLVSSSGFGDALISHM 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: 11.60
//
[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:

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:

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:

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:

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