Alignments for a candidate for icd in Synechococcus elongatus PCC 7942

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.2247.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.78
//
[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