Alignments for a candidate for icd in Desulfatiglans anilini DSM 4660

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Desulfatiglans anilini DSM 4660

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_084517751.1 H567_RS0121675 isocitrate dehydrogenase (NADP(+))

Query= SwissProt::Q9ZH99
         (427 letters)



>NCBI__GCF_000422285.1:WP_084517751.1
          Length = 421

 Score =  460 bits (1184), Expect = e-134
 Identities = 238/411 (57%), Positives = 295/411 (71%), Gaps = 3/411 (0%)

Query: 15  IKVPSQGEKITVNKAVLE-VPDRPIIPFIEGDGIGIDIAPVMKNVVDAAVEKSYAGKRKI 73
           ++ P+ G  IT +      VPD PIIPFIEGDG G DI    + V+DAAV K+Y GK+ I
Sbjct: 6   LETPTTGNTITWDSHGRPIVPDTPIIPFIEGDGTGPDIWRAARPVIDAAVRKTYGGKKAI 65

Query: 74  EWMEIYAGEKATKVYGKDNWLPDETLEAIKEYQVAIKGPLTTPVGGGIRSLNVALRQQLD 133
            W+E+ AG KA    G +  LP+ETLEA+  Y +AIKGPLTTPVGGG RSLNV LRQ+LD
Sbjct: 66  LWLELLAGAKAQDALGCECLLPEETLEALTRYGIAIKGPLTTPVGGGFRSLNVTLRQRLD 125

Query: 134 LYVCLRPVRYFTGVPSPVKTPEKVNMVIFRENSEDIYAGIEWPAGSPEAVKLINFLQNEM 193
           LY C+RPVRY  G+P+PV+ PEKV++VIFREN+ED+YAG+EW A SP A +++  +   +
Sbjct: 126 LYACIRPVRYVPGIPAPVRHPEKVDLVIFRENTEDVYAGVEWEAESPAAREILEQINARL 185

Query: 194 GVK-KIRFPETAGIGIKPVSKEGTSRLVRRAIQYAIDNDRDSVTLVHKGNIMKFTEGAFK 252
             + K   P  + +GIKP+S+  T RLV RAIQYA D+  DSVTLVHKGNIMK+TEGAF+
Sbjct: 186 SFEGKPLLPIDSAVGIKPMSRRNTQRLVARAIQYAADHHYDSVTLVHKGNIMKYTEGAFR 245

Query: 253 DWGYEVAVKEFGAKPL-DGGPWHVFENPKTGQKITIKDVIADAFLQQILLRPAEYSVIAT 311
           DWGY+ A + FG   L +   +  F       +I IKD IADA  QQ+LLRP EY V+AT
Sbjct: 246 DWGYQTAREMFGDLTLTEEELFADFGGKAPAGRIVIKDRIADAMFQQLLLRPEEYGVLAT 305

Query: 312 LNLNGDYISDALAAEVGGIGIAPGANLSDTVGLFEATHGTAPKYAGQDKVNPGSLILSAE 371
            NLNGDY+SDA AA+VGG+G+APGAN+ D   +FEATHG+APKYAG DKVNPGSLILS  
Sbjct: 306 PNLNGDYLSDAAAAQVGGLGMAPGANVGDRCAVFEATHGSAPKYAGLDKVNPGSLILSGV 365

Query: 372 MMLRYLGWKEAADLVVQGIEGAIESKTVTYDFARLMTGAKEVSTSQFGKAI 422
            MLR++GW EAADL+++G+   I    VTYD AR M  AKEVS S FG AI
Sbjct: 366 EMLRFMGWDEAADLILKGLRDTIGDGIVTYDLARQMENAKEVSCSAFGAAI 416


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: 588
Number of extensions: 21
Number of successful extensions: 3
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: 421
Length adjustment: 32
Effective length of query: 395
Effective length of database: 389
Effective search space:   153655
Effective search space used:   153655
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 WP_084517751.1 H567_RS0121675 (isocitrate dehydrogenase (NADP(+)))
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.3728951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-186  604.3   0.0   6.4e-186  604.1   0.0    1.0  1  NCBI__GCF_000422285.1:WP_084517751.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000422285.1:WP_084517751.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  604.1   0.0  6.4e-186  6.4e-186       3     416 ..       4     420 ..       2     421 .] 0.97

  Alignments for each domain:
  == domain 1  score: 604.1 bits;  conditional E-value: 6.4e-186
                             TIGR00183   3 ekvkppeeGekitlk.ngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGeka 74 
                                           +++++p++G+ it + +g+++vp+ piip+ieGdG+G di+ aa  v+daav k+y+g+k i w+e+ aG ka
  NCBI__GCF_000422285.1:WP_084517751.1   4 DRLETPTTGNTITWDsHGRPIVPDTPIIPFIEGDGTGPDIWRAARPVIDAAVRKTYGGKKAILWLELLAGAKA 76 
                                           578899*******96279******************************************************* PP

                             TIGR00183  75 yelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekv 147
                                            +  g e  lpe+tl+a+ +y +aikGplttpvGgG+rslnv+lrq+ldly+c+rpvry +g+p+pv++pekv
  NCBI__GCF_000422285.1:WP_084517751.1  77 QDALGCECLLPEETLEALTRYGIAIKGPLTTPVGGGFRSLNVTLRQRLDLYACIRPVRYVPGIPAPVRHPEKV 149
                                           ************************************************************************* PP

                             TIGR00183 148 dlvifrentediyaGiewaegseeakklikflknelkvk.kirlpedsGiGikpiseegtkrlvrkaieyaie 219
                                           dlvifrented+yaG+ew+++s  a+ +++ ++  l+ + k+ lp ds +Gikp+s+  t+rlv +ai+ya +
  NCBI__GCF_000422285.1:WP_084517751.1 150 DLVIFRENTEDVYAGVEWEAESPAAREILEQINARLSFEgKPLLPIDSAVGIKPMSRRNTQRLVARAIQYAAD 222
                                           ************************************97648999***************************** PP

                             TIGR00183 220 ndkksvtlvhkGnimkfteGafkdwGyelakkefgeevit.kalwdklknpeeGkkivvkdriadallqqilt 291
                                           ++ +svtlvhkGnimk+teGaf+dwGy+ a++ fg+  +t ++l+    ++ +  +iv+kdriada++qq+l+
  NCBI__GCF_000422285.1:WP_084517751.1 223 HHYDSVTLVHKGNIMKYTEGAFRDWGYQTAREMFGDLTLTeEELFADFGGKAPAGRIVIKDRIADAMFQQLLL 295
                                           ************************************99996788999999988888***************** PP

                             TIGR00183 292 rpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvlll 364
                                           rp+ey v+at+nlnGdylsda+aa+vGGlG+apGan+gd +a+feathG+apkyaGldkvnpgs+ilsgv +l
  NCBI__GCF_000422285.1:WP_084517751.1 296 RPEEYGVLATPNLNGDYLSDAAAAQVGGLGMAPGANVGDRCAVFEATHGSAPKYAGLDKVNPGSLILSGVEML 368
                                           ************************************************************************* PP

                             TIGR00183 365 eflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                           +f+Gw eaadli k+l  +i + +vtydlar m+ akev cs f+ ai +++
  NCBI__GCF_000422285.1:WP_084517751.1 369 RFMGWDEAADLILKGLRDTIGDGIVTYDLARQMENAKEVSCSAFGAAIQSRM 420
                                           **********************************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (421 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: 26.41
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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