GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Synechococcus elongatus PCC 7942

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Synpcc7942_1719 Synpcc7942_1719 isocitrate dehydrogenase

Query= BRENDA::A8YGS2
         (478 letters)



>FitnessBrowser__SynE:Synpcc7942_1719
          Length = 475

 Score =  791 bits (2043), Expect = 0.0
 Identities = 377/474 (79%), Positives = 421/474 (88%)

Query: 5   YEKITPPTTGSTITFSDGKPLVPDDPIIPFIRGDGTGVDIWPATAKVIDAAIAAAYGGQR 64
           YEKI PP+ GS I F  GKP+VPD+PIIPFIRGDGTGVDIWPAT +V+DAA+A AYGGQR
Sbjct: 2   YEKIQPPSEGSKIRFEAGKPIVPDNPIIPFIRGDGTGVDIWPATERVLDAAVAKAYGGQR 61

Query: 65  KIHWFKVYAGDEACEIYGTYQYLPQDTLTAIKEYGIAIKGPLTTPIGGGIRSLNVALRQI 124
           KI WFKVYAGDEAC++YGTYQYLP+DTLTAI+EYG+AIKGPLTTPIGGGIRSLNVALRQI
Sbjct: 62  KITWFKVYAGDEACDLYGTYQYLPEDTLTAIREYGVAIKGPLTTPIGGGIRSLNVALRQI 121

Query: 125 FDLYACVRPCRYYAGTPSPHKTPEKLDVIVYRENTEDIYLGIEWKQGTEIADKLINYLNT 184
           FDLYACVRPCRYY GTPSPH+TPE+LDV+VYRENTEDIYLGIEWKQG    D+LI  LN 
Sbjct: 122 FDLYACVRPCRYYTGTPSPHRTPEQLDVVVYRENTEDIYLGIEWKQGDPTGDRLIKLLNE 181

Query: 185 ELIPATPEHGKKQIPLDAGIGIKPISKTGSQRLVRRAIERALTLPKPKNQVTLVHKGNIM 244
           + IP +P  GKKQI LD+GIGIKPISKTGSQRL+RRAIE AL L   K  VTLVHKGNIM
Sbjct: 182 DFIPNSPSLGKKQIRLDSGIGIKPISKTGSQRLIRRAIEHALRLEGRKRHVTLVHKGNIM 241

Query: 245 KYTEGAFRDWGYELAKSEFRDVCVTEMESWILSNKEKNPDLSIEDNARMVEPGYDALTDE 304
           K+TEGAFRDWGYELA +EFR  CVTE ESWIL+N+E  PDLS+EDNAR++EPGYDA+T E
Sbjct: 242 KFTEGAFRDWGYELATTEFRTDCVTERESWILANQESKPDLSLEDNARLIEPGYDAMTPE 301

Query: 305 KKAKICQEVTSVLDAIWETHGNGQWKDKIMVNDRIADSIFQQIQTRPDEYSILATMNLNG 364
           K+A +  EV +VLD+I  THGNGQWK K++V+DRIADSIFQQIQTRP EYS+LATMNLNG
Sbjct: 302 KQAAVVAEVKAVLDSIGATHGNGQWKSKVLVDDRIADSIFQQIQTRPGEYSVLATMNLNG 361

Query: 365 DYLSDAAAAIVGGLGMGPGANIGDTCAIFEATHGTAPKHAGLDRINPGSVILSGVMMLEY 424
           DY+SDAAAA+VGGLGM PGANIGD  AIFEATHGTAPKHAGLDRINPGSVILSGVMMLEY
Sbjct: 362 DYISDAAAAVVGGLGMAPGANIGDEAAIFEATHGTAPKHAGLDRINPGSVILSGVMMLEY 421

Query: 425 MGWQEAADLIKKGIAAAVANRQVTYDLARLMEPPVNPPLKCSEFADAIISHFGD 478
           +GWQEAADLI KGI+ A+ANR+VTYDLARLMEP V+ PLKCSEFA+AI+ HF D
Sbjct: 422 LGWQEAADLITKGISQAIANREVTYDLARLMEPAVDQPLKCSEFAEAIVKHFDD 475


Lambda     K      H
   0.317    0.136    0.413 

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: 844
Number of extensions: 27
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: 478
Length of database: 475
Length adjustment: 33
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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: 51 (24.3 bits)

Align candidate Synpcc7942_1719 Synpcc7942_1719 (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.31197.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-219  713.1   0.0   6.1e-219  712.9   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1719  Synpcc7942_1719 isocitrate dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1719  Synpcc7942_1719 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.9   0.0  6.1e-219  6.1e-219       1     417 []       1     474 [.       1     474 [. 0.96

  Alignments for each domain:
  == domain 1  score: 712.9 bits;  conditional E-value: 6.1e-219
                                 TIGR00183   1 leekvkppeeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevy 69 
                                               ++ek++pp+eG+ki++++gk++vp+npiip+i+GdG+Gvdi+pa+++vldaav+kay+g++ki+wf+vy
  lcl|FitnessBrowser__SynE:Synpcc7942_1719   1 MYEKIQPPSEGSKIRFEAGKPIVPDNPIIPFIRGDGTGVDIWPATERVLDAAVAKAYGGQRKITWFKVY 69 
                                               79******************************************************************* PP

                                 TIGR00183  70 aGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvp 138
                                               aG++a++lyg+++ylpedtl+ai+ey vaikGplttp+GgGirslnvalrq++dly+c+rp+ryy+g+p
  lcl|FitnessBrowser__SynE:Synpcc7942_1719  70 AGDEACDLYGTYQYLPEDTLTAIREYGVAIKGPLTTPIGGGIRSLNVALRQIFDLYACVRPCRYYTGTP 138
                                               ********************************************************************* PP

                                 TIGR00183 139 spvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpe.....dsGiGikpis 202
                                               sp+++pe++d+v++rentediy+Giew++g     +lik l+++++++ ++l++     dsGiGikpis
  lcl|FitnessBrowser__SynE:Synpcc7942_1719 139 SPHRTPEQLDVVVYRENTEDIYLGIEWKQGDPTGDRLIKLLNEDFIPNSPSLGKkqirlDSGIGIKPIS 207
                                               *************************************************9999989999********** PP

                                 TIGR00183 203 eegtkrlvrkaieyaien..dkksvtlvhkGnimkfteGafkdwGyelakkefgeevit....kalwdk 265
                                               ++g++rl+r+aie+a++    k+ vtlvhkGnimkfteGaf+dwGyela++ef+ +++t    ++l ++
  lcl|FitnessBrowser__SynE:Synpcc7942_1719 208 KTGSQRLIRRAIEHALRLegRKRHVTLVHKGNIMKFTEGAFRDWGYELATTEFRTDCVTeresWILANQ 276
                                               ***************998657899***********************************7555555555 PP

                                 TIGR00183 266 lknp..eeGk............................................kivvkdriadallqq 288
                                               +++p  +                                               k++v+driad+++qq
  lcl|FitnessBrowser__SynE:Synpcc7942_1719 277 ESKPdlS--LednarliepgydamtpekqaavvaevkavldsigathgngqwksKVLVDDRIADSIFQQ 343
                                               5555550..255556777777************************************************ PP

                                 TIGR00183 289 iltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvi 357
                                               i+trp ey+v+atmnlnGdy+sda+aa+vGGlG+apGanigde+aifeathGtapk+aGld++npgsvi
  lcl|FitnessBrowser__SynE:Synpcc7942_1719 344 IQTRPGEYSVLATMNLNGDYISDAAAAVVGGLGMAPGANIGDEAAIFEATHGTAPKHAGLDRINPGSVI 412
                                               ********************************************************************* PP

                                 TIGR00183 358 lsgvllleflGwkeaadlivkalekaiaskevtydlarlmdg..akevkcsefaeaivenld 417
                                               lsgv++le+lGw+eaadli k++ +aia++evtydlarlm++  ++++kcsefaeaiv+++d
  lcl|FitnessBrowser__SynE:Synpcc7942_1719 413 LSGVMMLEYLGWQEAADLITKGISQAIANREVTYDLARLMEPavDQPLKCSEFAEAIVKHFD 474
                                               ******************************************88899************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (475 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: 10.92
//
[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