Alignments for a candidate for icd in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Burkholderia phytofirmans PsJN

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate BPHYT_RS15730 BPHYT_RS15730 isocitrate dehydrogenase

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__BFirm:BPHYT_RS15730
          Length = 418

 Score =  654 bits (1687), Expect = 0.0
 Identities = 320/418 (76%), Positives = 368/418 (88%)

Query: 1   MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK 60
           M YQ I+VP  GDKITVNAD SL+V   PIIP+IEGDG G+DI+PVMIKVVDAAVEKAY 
Sbjct: 1   MPYQHIKVPTGGDKITVNADFSLNVSDQPIIPYIEGDGTGLDITPVMIKVVDAAVEKAYA 60

Query: 61  GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL 120
           G++KI WME+YAGEK+T+VY  D WLP+ETL  +++YVVSIKGPLTTPVGGGIRSLNVAL
Sbjct: 61  GKKKIHWMEIYAGEKSTKVYGPDVWLPEETLQVLKEYVVSIKGPLTTPVGGGIRSLNVAL 120

Query: 121 RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF 180
           RQ+LDLYVC RPV++F+GVPSPV++P   +MVIFRENSEDIYAG+EW A S +A+KVIKF
Sbjct: 121 RQELDLYVCLRPVQYFKGVPSPVREPEKTNMVIFRENSEDIYAGIEWPAESEQAKKVIKF 180

Query: 181 LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE 240
           L EEMGVKKIRF +  GIGIKPVS+EGT+RLVRKA+QYA+DN+R SVTLVHKGNIMKFTE
Sbjct: 181 LREEMGVKKIRFPDTSGIGIKPVSREGTERLVRKAIQYAIDNERRSVTLVHKGNIMKFTE 240

Query: 241 GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV 300
           GAF+D+GY +A+ EF AEL+DGGPWM+ KNPKTG ++V+KDVIADA LQQILLRPAEYDV
Sbjct: 241 GAFRDYGYALAQKEFAAELIDGGPWMKIKNPKTGGDIVLKDVIADAFLQQILLRPAEYDV 300

Query: 301 IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL 360
           IATLNLNGDY+SDALAA+VGGIGIAPGAN+SDSVAMFEATHGTAPKYAG+D VNPGS IL
Sbjct: 301 IATLNLNGDYVSDALAAQVGGIGIAPGANMSDSVAMFEATHGTAPKYAGKDYVNPGSEIL 360

Query: 361 SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           SAEMMLRH+GWTEAADLIIK    +I  K VTYDF RLM+GAT +SCS FG  +I  M
Sbjct: 361 SAEMMLRHLGWTEAADLIIKSMEKSILQKRVTYDFARLMEGATQVSCSGFGQVLIENM 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: 697
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 BPHYT_RS15730 BPHYT_RS15730 (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.21782.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-224  729.8   0.7   4.8e-224  729.7   0.7    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS15730  BPHYT_RS15730 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS15730  BPHYT_RS15730 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.7   0.7  4.8e-224  4.8e-224       2     416 ..       3     418 .]       2     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 729.7 bits;  conditional E-value: 4.8e-224
                                TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevya 70 
                                              ++++k+p+ G+kit++++  l+v ++piipyieGdG+G di+p +ikv+daavekay g+kki w+e+ya
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730   3 YQHIKVPTGGDKITVNADfSLNVSDQPIIPYIEGDGTGLDITPVMIKVVDAAVEKAYAGKKKIHWMEIYA 72 
                                              57899**********876379************************************************* PP

                                TIGR00183  71 GekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpsp 140
                                              Gek++++yg + +lpe+tl+++key v+ikGplttpvGgGirslnvalrqeldlyvclrpv+y+kgvpsp
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730  73 GEKSTKVYGPDVWLPEETLQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVQYFKGVPSP 142
                                              ********************************************************************** PP

                                TIGR00183 141 vkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlv 210
                                              v+epek+++vifren+ediyaGiew ++se+akk+ikfl++e++vkkir+p++sGiGikp+s+egt+rlv
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730 143 VREPEKTNMVIFRENSEDIYAGIEWPAESEQAKKVIKFLREEMGVKKIRFPDTSGIGIKPVSREGTERLV 212
                                              ********************************************************************** PP

                                TIGR00183 211 rkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdr 280
                                              rkai+yai+n+++svtlvhkGnimkfteGaf+d+Gy+la+kef +e+i+ ++w k+knp++G +iv+kd+
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730 213 RKAIQYAIDNERRSVTLVHKGNIMKFTEGAFRDYGYALAQKEFAAELIDGGPWMKIKNPKTGGDIVLKDV 282
                                              ********************************************************************** PP

                                TIGR00183 281 iadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldk 350
                                              iada+lqqil+rp+eydviat+nlnGdy+sdalaa+vGG+GiapGan++d+va+feathGtapkyaG+d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730 283 IADAFLQQILLRPAEYDVIATLNLNGDYVSDALAAQVGGIGIAPGANMSDSVAMFEATHGTAPKYAGKDY 352
                                              ********************************************************************** PP

                                TIGR00183 351 vnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                              vnpgs ils++++l++lGw+eaadli+k++ek+i +k+vtyd+arlm+ga++v cs f+++++en+
  lcl|FitnessBrowser__BFirm:BPHYT_RS15730 353 VNPGSEILSAEMMLRHLGWTEAADLIIKSMEKSILQKRVTYDFARLMEGATQVSCSGFGQVLIENM 418
                                              *****************************************************************8 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.17
//
[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