Alignments for a candidate for icd in Sphaerochaeta globosa Buddy

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Sphaerochaeta globosa Buddy

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_013606868.1 SPIBUDDY_RS06035 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::Q9ZH99
         (427 letters)



>NCBI__GCF_000190435.1:WP_013606868.1
          Length = 409

 Score =  476 bits (1226), Expect = e-139
 Identities = 246/406 (60%), Positives = 303/406 (74%), Gaps = 10/406 (2%)

Query: 24  ITVNKAVLEVPDRPIIPFIEGDGIGIDIAPVMKNVVDAAVEKSYAGKRKIEWMEIYAGEK 83
           I++    L VPD   IP IEGDG+G +I  VMKNVVD AV+K+Y G+R I+++E+ AG+K
Sbjct: 5   ISIENGKLSVPDHVTIPCIEGDGVGPEITSVMKNVVDQAVQKAYQGRRSIQFIEVLAGQK 64

Query: 84  ATKVYGKDNWLPDETLEAIKEYQVAIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRY 143
           A    G   +LP+ET+EA+  Y+VAIKGPLTTPVG GIRSLNV LRQ LDLYVCLRPV Y
Sbjct: 65  AKDTVG--TYLPEETMEAVNTYKVAIKGPLTTPVGKGIRSLNVTLRQSLDLYVCLRPVEY 122

Query: 144 FTGVPSPVKTPEKVNMVIFRENSEDIYAGIEWPAGSPEAVKLINFLQNEMGVKKIRFPET 203
           F GVPSPVK PEKV+MV+FREN+EDIYAGIEW AGS    K++NFL +EMGVK IRFP +
Sbjct: 123 FAGVPSPVKHPEKVDMVVFRENTEDIYAGIEWEAGSSGVQKVLNFLTDEMGVKNIRFPNS 182

Query: 204 AGIGIKPVSKEGTSRLVRRAIQYAIDNDRDSVTLVHKGNIMKFTEGAFKDWGYEVAVKEF 263
           + +GIKPVS+EG+ RL+R AI YA++++R +VTLVHKGNIMKFTEG F  WGYE+A +EF
Sbjct: 183 SALGIKPVSREGSERLIRSAITYALEHNRRNVTLVHKGNIMKFTEGGFNAWGYELAKREF 242

Query: 264 GAKPLDGGPWHVFENPKTGQKITIKDVIADAFLQQILLRPAEYSVIATLNLNGDYISDAL 323
           GA+  +     VF     G+ + I+D I DAFLQ ILL+P  Y VIATLNLNGDY+SDAL
Sbjct: 243 GAQ--EDAKKRVFIPRTEGEPLYIQDCICDAFLQNILLKPEAYDVIATLNLNGDYVSDAL 300

Query: 324 AAEVGGIGIAPGANLSDTVG--LFEATHGTAPKYAGQDKVNPGSLILSAEMMLRYLGWKE 381
           AAEVGGIGIAPGAN++   G  +FEATHGTAP  AG+D VNP SL+LSA MML YLGW E
Sbjct: 301 AAEVGGIGIAPGANINYDNGYAIFEATHGTAPDIAGKDLVNPLSLVLSAVMMLNYLGWDE 360

Query: 382 AADLVVQGIEGAIESKTVTYDFARLMT----GAKEVSTSQFGKAII 423
           AA L+   +  AIE+  VT DF + M        ++ T  FG+ ++
Sbjct: 361 AASLIKCAVGKAIEAGAVTSDFYQAMVKEGRACTQLGTQAFGQRLV 406


Lambda     K      H
   0.317    0.136    0.396 

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: 534
Number of extensions: 22
Number of successful extensions: 5
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: 427
Length of database: 409
Length adjustment: 32
Effective length of query: 395
Effective length of database: 377
Effective search space:   148915
Effective search space used:   148915
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 WP_013606868.1 SPIBUDDY_RS06035 (NADP-dependent 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.3764029.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-178  578.7   0.2   3.6e-178  578.5   0.2    1.0  1  NCBI__GCF_000190435.1:WP_013606868.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000190435.1:WP_013606868.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.5   0.2  3.6e-178  3.6e-178      12     414 ..       3     407 ..       1     409 [] 0.96

  Alignments for each domain:
  == domain 1  score: 578.5 bits;  conditional E-value: 3.6e-178
                             TIGR00183  12 ekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekayelygeeeyl 84 
                                           + i+++ngkl vp++  ip ieGdG+G +i++ +++v+d av+kay+g + i+++ev aG+ka + +g  +yl
  NCBI__GCF_000190435.1:WP_013606868.1   3 KAISIENGKLSVPDHVTIPCIEGDGVGPEITSVMKNVVDQAVQKAYQGRRSIQFIEVLAGQKAKDTVG--TYL 73 
                                           5799****************************************************************..9** PP

                             TIGR00183  85 pedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifrente 157
                                           pe+t++a++ ykvaikGplttpvG+Girslnv+lrq ldlyvclrpv y+ gvpspvk+pekvd+v+frente
  NCBI__GCF_000190435.1:WP_013606868.1  74 PEETMEAVNTYKVAIKGPLTTPVGKGIRSLNVTLRQSLDLYVCLRPVEYFAGVPSPVKHPEKVDMVVFRENTE 146
                                           ************************************************************************* PP

                             TIGR00183 158 diyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhk 230
                                           diyaGiew++gs +++k+++fl +e++vk+ir+p++s +Gikp+s+eg++rl+r ai+ya+e++++ vtlvhk
  NCBI__GCF_000190435.1:WP_013606868.1 147 DIYAGIEWEAGSSGVQKVLNFLTDEMGVKNIRFPNSSALGIKPVSREGSERLIRSAITYALEHNRRNVTLVHK 219
                                           ************************************************************************* PP

                             TIGR00183 231 GnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmn 303
                                           GnimkfteG f+ wGyelak+efg++   +a+      + eG+ + ++d i da+lq+il++p+ ydviat+n
  NCBI__GCF_000190435.1:WP_013606868.1 220 GNIMKFTEGGFNAWGYELAKREFGAQE--DAKKRVFIPRTEGEPLYIQDCICDAFLQNILLKPEAYDVIATLN 290
                                           ************************985..344444455579******************************** PP

                             TIGR00183 304 lnGdylsdalaalvGGlGiapGanigdeva..ifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaad 374
                                           lnGdy+sdalaa vGG+GiapGani+++ +  ifeathGtap  aG+d vnp s++ls+v++l++lGw eaa 
  NCBI__GCF_000190435.1:WP_013606868.1 291 LNGDYVSDALAAEVGGIGIAPGANINYDNGyaIFEATHGTAPDIAGKDLVNPLSLVLSAVMMLNYLGWDEAAS 363
                                           **************************986555***************************************** PP

                             TIGR00183 375 livkalekaiaskevtydlarlmdg....akevkcsefaeaive 414
                                           li+ a++kai++  vt d+ + m       ++++++ f++ +v 
  NCBI__GCF_000190435.1:WP_013606868.1 364 LIKCAVGKAIEAGAVTSDFYQAMVKegraCTQLGTQAFGQRLVA 407
                                           *******************9999543355689999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (409 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.28
//
[ok]

This GapMind analysis is from Sep 24 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