Alignments for a candidate for icd in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Dinoroseobacter shibae DFL-12

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate 3608592 Dshi_1986 isocitrate dehydrogenase, NADP-dependent (RefSeq)

Query= BRENDA::B2ZAA4
         (739 letters)



>FitnessBrowser__Dino:3608592
          Length = 722

 Score =  767 bits (1980), Expect = 0.0
 Identities = 411/733 (56%), Positives = 501/733 (68%), Gaps = 21/733 (2%)

Query: 2   TDSTIIYTHTDEAPALATYSFLPVVRAYASQAGVAVETRDISLAGRIIALFPEYLTEDQR 61
           T+  I+YT  DEAP LA+ S LP+++A+A+ AGV+V  +DISLA RI+A           
Sbjct: 5   TNPDIVYTTVDEAPELASASLLPIIQAFAAPAGVSVGKKDISLAARILAAVAG------- 57

Query: 62  IPDALAELGELAKTPAANIIKLPNISASIPQLKAAVAELQGQGYALPAYPDDPKTDEERD 121
            PD LAELG L KTP AN+IKLPNISAS PQL AA+AELQ QG+ +PAYP +P T EE  
Sbjct: 58  APDHLAELGGLVKTPTANVIKLPNISASQPQLDAAIAELQSQGHDIPAYPANPTTPEEER 117

Query: 122 IRARYDKVKGSAVNPVLREGNSDRRAPASVKNYAKTHPHRMGAWTGESKTNVATMGENDF 181
           I+A YD VKGSAVNPVLREGNSDRRA  +VKNYA+ +PHRMG WT +SKT V TMG  DF
Sbjct: 118 IKAAYDAVKGSAVNPVLREGNSDRRAAQAVKNYARANPHRMGEWTADSKTTVMTMGARDF 177

Query: 182 RSTEKSAVI--AEDGTLRIELVGDDGTTTVLRESVPVKKDEVVDASVLRVAALREFLTAQ 239
            S E S  I  A+ G  RIE VG DGTT VL+E VP+    V DA+ + VAALR+FL   
Sbjct: 178 CSNETSTTITAAQAGPARIEFVGADGTT-VLKEGVPLDAGTVCDATFMSVAALRDFLAET 236

Query: 240 VARAKAEGILYSVHLKATMMKVSDPIIFGHVVRAFFPKTFAQYGDVLAKAGLTPNDGLGG 299
           ++  K  G+L+S+HLKATMMKVSDPIIFGH V  FF + F ++ ++    G     GLG 
Sbjct: 237 ISATKEAGVLWSIHLKATMMKVSDPIIFGHAVEVFFAELFEKHPELTGARG-----GLGT 291

Query: 300 IYKGLESLPEGAEIKASFDAELAEGPELAMVDSDKGITNLHVPSDVIIDASMPAMIRTSG 359
           +  G         + A + A L + P + MV+SD G+TNLHVPSDVIIDAS+PA+IR  G
Sbjct: 292 VLNGASDA-----VLADYQAVLDKQPPMYMVNSDTGLTNLHVPSDVIIDASLPAIIRAGG 346

Query: 360 HMWGADGGEHDALAVIPDSSYAGVYQAVIEDCRANGAYDPSTMGSVPNVGLMAQKAEEYG 419
             WG DG E D + VIPDSSYA VY   IE  + +G  D +T G+V N+GLMAQKAEEYG
Sbjct: 347 KGWGPDGNEADTVCVIPDSSYAPVYAETIEFFKKHGKLDVTTAGTVQNLGLMAQKAEEYG 406

Query: 420 SHDKTFEIPTTGTVRLVDAAGNAVLEQTVSAGDIFRACQTKDAPIRDWVKLAVTRARATG 479
           SH  TFE P  GT+R++ A G+ +    V  GDI+R+C  K API DWVKLA+ R + TG
Sbjct: 407 SHPTTFEAPADGTIRMIAANGDVLHSHEVEKGDIWRSCTAKKAPIEDWVKLAIERQKLTG 466

Query: 480 DPAVFWLDEGRAHDANLIAKVKQYLTEHDTEGLDIRILDPVEATKLSVERIRRGENTISV 539
             A+FWL+  RAHDA LI  V   L           I+ P EAT  S+E I +GENTI++
Sbjct: 467 YRAIFWLNADRAHDAELIKHVTPILEAAGVAD-KFEIMSPAEATVASLETITKGENTIAI 525

Query: 540 TGNVLRDYLTDLFPILELGTSAKMLSVVPLMAGGGLFETGAGGSAPKHVQQLVKEDYLRW 599
           TGNVLRDYLTDLFPILELGTSAKMLS+V LM GGGLFETGAGGSAPKHVQQL  E++LRW
Sbjct: 526 TGNVLRDYLTDLFPILELGTSAKMLSIVKLMQGGGLFETGAGGSAPKHVQQLQAENHLRW 585

Query: 600 DSLGEFFALVPSLEKYAEATGNGKAKVLADTLDRATATFLNEDKSPTRRVGGIDNRGSHF 659
           DSLGEF AL  S +  A++  N KA VL D ++ AT   L  D+SP R+VG  DNR SH+
Sbjct: 586 DSLGEFCALGESFKFLAQSRDNAKAGVLGDAVEAATQKVLEFDRSPGRKVGQPDNRASHY 645

Query: 660 YLSLYWAQELAKQTDDADLAKAFAPLAETLTASEQKIVEELNAVQGKPAEIGGYYQPDPA 719
           + + YWA+ LA Q  DA++A  FAP+A  L  +E+ I+ EL A  G PA+ GGYY  DPA
Sbjct: 646 WFARYWAEALAAQDKDAEIAAHFAPIAAKLAENEETILAELAAGAGTPADTGGYYHNDPA 705

Query: 720 KAAKIMRPSTTWN 732
           K A +MRPS T N
Sbjct: 706 KVAAVMRPSPTLN 718


Lambda     K      H
   0.315    0.132    0.375 

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: 1357
Number of extensions: 50
Number of successful extensions: 6
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: 739
Length of database: 722
Length adjustment: 40
Effective length of query: 699
Effective length of database: 682
Effective search space:   476718
Effective search space used:   476718
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: 42 (22.0 bits)
S2: 55 (25.8 bits)

Align candidate 3608592 Dshi_1986 (isocitrate dehydrogenase, NADP-dependent (RefSeq))
to HMM TIGR00178 (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/TIGR00178.hmm
# target sequence database:        /tmp/gapView.12425.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00178  [M=744]
Accession:   TIGR00178
Description: monomer_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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-299  981.7   0.3   2.2e-299  981.3   0.3    1.0  1  lcl|FitnessBrowser__Dino:3608592  Dshi_1986 isocitrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608592  Dshi_1986 isocitrate dehydrogenase, NADP-dependent (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  981.3   0.3  2.2e-299  2.2e-299       5     739 ..       6     721 ..       2     722 .] 0.97

  Alignments for each domain:
  == domain 1  score: 981.3 bits;  conditional E-value: 2.2e-299
                         TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpean 81 
                                       ++ i+yt  deap la+ sllpi++afaa+aG++v  +disla+rila            +d+laelG l ktp an
  lcl|FitnessBrowser__Dino:3608592   6 NPDIVYTTVDEAPELASASLLPIIQAFAAPAGVSVGKKDISLAARILAAVAG-------APDHLAELGGLVKTPTAN 75 
                                       689*********************************************9764.......69**************** PP

                         TIGR00178  82 iiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkeyar 158
                                       +iklpnisas pql+aai elq++G+d+p yp++p+t ee+ ika y+++kGsavnpvlreGnsdrra +avk+yar
  lcl|FitnessBrowser__Dino:3608592  76 VIKLPNISASQPQLDAAIAELQSQGHDIPAYPANPTTPEEERIKAAYDAVKGSAVNPVLREGNSDRRAAQAVKNYAR 152
                                       ***************************************************************************** PP

                         TIGR00178 159 khphkmGewsadskshvahmdagdfyaseksvlldaaee..vkieliakdGketvlkaklklldgevidssvlskka 233
                                        +ph+mGew+adsk+ v +m a df ++e s ++ aa+    +ie++ +dG+ tvlk+ ++l++g v d++++s  a
  lcl|FitnessBrowser__Dino:3608592 153 ANPHRMGEWTADSKTTVMTMGARDFCSNETSTTITAAQAgpARIEFVGADGT-TVLKEGVPLDAGTVCDATFMSVAA 228
                                       ********************************9998765338*********6.79********************** PP

                         TIGR00178 234 lvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslp 310
                                       l++fl+e i+ +ke gvl s+hlkatmmkvsdpi+fGh+v vf+++ f kh el  +       Gl+ ++       
  lcl|FitnessBrowser__Dino:3608592 229 LRDFLAETISATKEAGVLWSIHLKATMMKVSDPIIFGHAVEVFFAELFEKHPELTGAR-----GGLGTVLN------ 294
                                       ****************************************************987554.....59998864...... PP

                         TIGR00178 311 aakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagv 387
                                        +  + + ad ++v++++p + mv+sd G+tnlhvpsdvi+das+pa+ira+Gk +g+dg++ dt  vipdssya v
  lcl|FitnessBrowser__Dino:3608592 295 -GASDAVLADYQAVLDKQPPMYMVNSDTGLTNLHVPSDVIIDASLPAIIRAGGKGWGPDGNEADTVCVIPDSSYAPV 370
                                       .346889********************************************************************** PP

                         TIGR00178 388 yqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvk 464
                                       y + ie+ kk+G++d tt Gtv n+GlmaqkaeeyGsh  tfe +adG++r++ ++G+vl  +eve+gdiwr c +k
  lcl|FitnessBrowser__Dino:3608592 371 YAETIEFFKKHGKLDVTTAGTVQNLGLMAQKAEEYGSHPTTFEAPADGTIRMIAANGDVLHSHEVEKGDIWRSCTAK 447
                                       ***************************************************************************** PP

                         TIGR00178 465 dapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedti 541
                                        api+dwvkla+ r +l+g  a+fwl+ +rahd+elik+v   l+         +i+sp +at  sle i++Ge+ti
  lcl|FitnessBrowser__Dino:3608592 448 KAPIEDWVKLAIERQKLTGYRAIFWLNADRAHDAELIKHVTPILEAAGVA-DKFEIMSPAEATVASLETITKGENTI 523
                                       *****************************************999876554.4799********************** PP

                         TIGR00178 542 svtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaasleh 618
                                       ++tGnvlrdyltdlfpilelGtsakmls+v lm+GGGlfetGaGGsapkhvqql+ enhlrwdslGef al++s++ 
  lcl|FitnessBrowser__Dino:3608592 524 AITGNVLRDYLTDLFPILELGTSAKMLSIVKLMQGGGLFETGAGGSAPKHVQQLQAENHLRWDSLGEFCALGESFKF 600
                                       ***************************************************************************** PP

                         TIGR00178 619 vavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtk 695
                                       +a++ +n+ka vl+d+++aat+k+l+ ++sp rkvG+ dnr s++++a+ywa++laaq +d+e+aa+fa++a  l++
  lcl|FitnessBrowser__Dino:3608592 601 LAQSRDNAKAGVLGDAVEAATQKVLEFDRSPGRKVGQPDNRASHYWFARYWAEALAAQDKDAEIAAHFAPIAAKLAE 677
                                       ***************************************************************************** PP

                         TIGR00178 696 neekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnail 739
                                       nee+i aelaa  G++ d gGyy+ d  ++ +v+rps t+nai+
  lcl|FitnessBrowser__Dino:3608592 678 NEETILAELAAGAGTPADTGGYYHNDPAKVAAVMRPSPTLNAII 721
                                       *****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (722 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 7.92
//
[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:

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