Alignments for a candidate for icd in Jeotgalibacillus soli P9

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Jeotgalibacillus soli P9

Align isocitrate dehydrogenase; EC 1.1.1.42 (characterized)
to candidate WP_041090732.1 KP78_RS16950 NADP-dependent isocitrate dehydrogenase

Query= CharProtDB::CH_005143
         (423 letters)



>NCBI__GCF_000829435.1:WP_041090732.1
          Length = 422

 Score =  743 bits (1918), Expect = 0.0
 Identities = 367/422 (86%), Positives = 395/422 (93%)

Query: 1   MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKE 60
           M+QGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIW +AS+VL+AAV+KAY GEKK+ WKE
Sbjct: 1   MSQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWASASRVLDAAVDKAYNGEKKVVWKE 60

Query: 61  VYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVCLR 120
           V AGEKA+N+TGEWLP  TLD I EYFIAIKGPLTTPVGGGIRSLNVALRQ+LDLF CLR
Sbjct: 61  VLAGEKAFNETGEWLPQATLDDINEYFIAIKGPLTTPVGGGIRSLNVALRQQLDLFTCLR 120

Query: 121 PVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIR 180
           PVRYF GVPSPVKRPEDTDMVIFRENTEDIYAGIEYA+G++EV KLI FL+N + V  IR
Sbjct: 121 PVRYFEGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAEGTDEVNKLIDFLKNVMGVKNIR 180

Query: 181 FPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELA 240
           FPETSGIGIKPVS+EGT+RLVR+AI+YAI  GRKSVTLVHKGNIMKFTEGAFKNWGYELA
Sbjct: 181 FPETSGIGIKPVSKEGTNRLVRSAINYAITEGRKSVTLVHKGNIMKFTEGAFKNWGYELA 240

Query: 241 EKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEF 300
           E+E+GDKVFTWAQYD+I +EQG +AANKAQ++AE AGKIIIKDSIADIFLQQILTRP EF
Sbjct: 241 EQEFGDKVFTWAQYDKIKDEQGAEAANKAQADAEVAGKIIIKDSIADIFLQQILTRPAEF 300

Query: 301 DVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPS 360
           DVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAG DKVNPS
Sbjct: 301 DVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGQDKVNPS 360

Query: 361 SVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIK 420
           SVILSGVLLLEHLGW+EAA LV+ SMEKTIASKVVTYDFARLMDGATEVKCSEFG  LI+
Sbjct: 361 SVILSGVLLLEHLGWHEAAKLVLTSMEKTIASKVVTYDFARLMDGATEVKCSEFGSALIE 420

Query: 421 NM 422
           NM
Sbjct: 421 NM 422


Lambda     K      H
   0.315    0.134    0.387 

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: 657
Number of extensions: 22
Number of successful extensions: 2
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: 423
Length of database: 422
Length adjustment: 32
Effective length of query: 391
Effective length of database: 390
Effective search space:   152490
Effective search space used:   152490
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: 50 (23.9 bits)

Align candidate WP_041090732.1 KP78_RS16950 (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.3354666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-224  730.1   1.4   3.9e-224  729.9   1.4    1.0  1  NCBI__GCF_000829435.1:WP_041090732.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000829435.1:WP_041090732.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.9   1.4  3.9e-224  3.9e-224       9     416 ..       2     422 .]       1     422 [] 0.98

  Alignments for each domain:
  == domain 1  score: 729.9 bits;  conditional E-value: 3.9e-224
                             TIGR00183   9 eeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekayelygee 81 
                                           ++Gekit++ng+l+vpnnpiip+ieGdG+G di+++a++vldaav+kay+gekk++w+ev aGeka++ +g  
  NCBI__GCF_000829435.1:WP_041090732.1   2 SQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWASASRVLDAAVDKAYNGEKKVVWKEVLAGEKAFNETG-- 72 
                                           69*********************************************************************.. PP

                             TIGR00183  82 eylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifre 154
                                           e+lp+ tld i+ey +aikGplttpvGgGirslnvalrq+ldl++clrpvry++gvpspvk+pe++d+vifre
  NCBI__GCF_000829435.1:WP_041090732.1  73 EWLPQATLDDINEYFIAIKGPLTTPVGGGIRSLNVALRQQLDLFTCLRPVRYFEGVPSPVKRPEDTDMVIFRE 145
                                           9************************************************************************ PP

                             TIGR00183 155 ntediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtl 227
                                           ntediyaGie+aeg++e++kli flkn ++vk+ir+pe+sGiGikp+s+egt+rlvr ai+yai++ +ksvtl
  NCBI__GCF_000829435.1:WP_041090732.1 146 NTEDIYAGIEYAEGTDEVNKLIDFLKNVMGVKNIRFPETSGIGIKPVSKEGTNRLVRSAINYAITEGRKSVTL 218
                                           ************************************************************************* PP

                             TIGR00183 228 vhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGk..............kivvkdriadall 286
                                           vhkGnimkfteGafk+wGyela++efg++v+t+a++dk+k++ +G               ki++kd+iad++l
  NCBI__GCF_000829435.1:WP_041090732.1 219 VHKGNIMKFTEGAFKNWGYELAEQEFGDKVFTWAQYDKIKDE-QGAeaankaqadaevagKIIIKDSIADIFL 290
                                           ****************************************95.55557788889999999************* PP

                             TIGR00183 287 qqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdeva..ifeathGtapkyaGldkvnpgsvi 357
                                           qqiltrp+e+dv+atmnlnGdy+sdalaa+vGG+GiapGani++e++  ifeathGtapkyaG+dkvnp+svi
  NCBI__GCF_000829435.1:WP_041090732.1 291 QQILTRPAEFDVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGhaIFEATHGTAPKYAGQDKVNPSSVI 363
                                           ********************************************99777************************ PP

                             TIGR00183 358 lsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                           lsgvllle+lGw+eaa+l+  ++ek+iask+vtyd+arlmdga+evkcsef++a++en+
  NCBI__GCF_000829435.1:WP_041090732.1 364 LSGVLLLEHLGWHEAAKLVLTSMEKTIASKVVTYDFARLMDGATEVKCSEFGSALIENM 422
                                           **********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (422 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.87
//
[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