Alignments for a candidate for icd in Hafnia paralvei ATCC 29927

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Hafnia paralvei ATCC 29927

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42); [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) (characterized)
to candidate WP_004090093.1 M988_RS10665 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::P08200
         (416 letters)



>NCBI__GCF_001655005.1:WP_004090093.1
          Length = 417

 Score =  779 bits (2011), Expect = 0.0
 Identities = 382/417 (91%), Positives = 403/417 (96%), Gaps = 1/417 (0%)

Query: 1   MESKVVVPAQGKKITLQ-NGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKG 59
           MESKVVVPA+GKKIT+   GKL VP NP+IP+IEGDGIGVDVTPAM+KVVDAAV KAYKG
Sbjct: 1   MESKVVVPAEGKKITVDAQGKLVVPHNPVIPFIEGDGIGVDVTPAMIKVVDAAVNKAYKG 60

Query: 60  ERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALR 119
           ERKISWMEIYTGEKSTQVYG+DVWLP ETLDLIR+YRVAIKGPLTTPVGGGIRSLNVALR
Sbjct: 61  ERKISWMEIYTGEKSTQVYGKDVWLPEETLDLIRDYRVAIKGPLTTPVGGGIRSLNVALR 120

Query: 120 QELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFL 179
           Q+LDLYICLRPVRYYQGTPSPVK PELTDMVIFRENSEDIYAGIEWKADSA+A+KVIKFL
Sbjct: 121 QQLDLYICLRPVRYYQGTPSPVKQPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFL 180

Query: 180 REEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEG 239
           R+EMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAI NDRDS+TLVHKGNIMKFTEG
Sbjct: 181 RDEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAITNDRDSLTLVHKGNIMKFTEG 240

Query: 240 AFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVI 299
           AFKDWGYQLAREEFGGELIDGGPW+K+KNP TGK+I++KDVIADAFLQQILLRPAEYDVI
Sbjct: 241 AFKDWGYQLAREEFGGELIDGGPWVKIKNPKTGKDIIVKDVIADAFLQQILLRPAEYDVI 300

Query: 300 ACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILS 359
           ACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILS
Sbjct: 301 ACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILS 360

Query: 360 AEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
           AEMMLRHM W EAADLIVKGMEGAI AKTVTYDFER ++GAKLLKCSEFGDAII++M
Sbjct: 361 AEMMLRHMEWFEAADLIVKGMEGAIAAKTVTYDFERQLEGAKLLKCSEFGDAIIKHM 417


Lambda     K      H
   0.318    0.138    0.408 

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: 769
Number of extensions: 19
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: 416
Length of database: 417
Length adjustment: 31
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_004090093.1 M988_RS10665 (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.760480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-238  775.3   0.8   7.8e-238  775.1   0.8    1.0  1  NCBI__GCF_001655005.1:WP_004090093.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001655005.1:WP_004090093.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  775.1   0.8  7.8e-238  7.8e-238       1     416 [.       1     417 []       1     417 [] 0.99

  Alignments for each domain:
  == domain 1  score: 775.1 bits;  conditional E-value: 7.8e-238
                             TIGR00183   1 leekvkppeeGekitlk.ngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGe 72 
                                           +e+kv++p+eG+kit++ +gklvvp+np+ip+ieGdGiGvd++pa+ikv+daav+kaykge+ki+w+e+y+Ge
  NCBI__GCF_001655005.1:WP_004090093.1   1 MESKVVVPAEGKKITVDaQGKLVVPHNPVIPFIEGDGIGVDVTPAMIKVVDAAVNKAYKGERKISWMEIYTGE 73 
                                           689*************7369***************************************************** PP

                             TIGR00183  73 kayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepe 145
                                           k++++yg++ +lpe+tld+i++y+vaikGplttpvGgGirslnvalrq+ldly+clrpvryy+g+pspvk+pe
  NCBI__GCF_001655005.1:WP_004090093.1  74 KSTQVYGKDVWLPEETLDLIRDYRVAIKGPLTTPVGGGIRSLNVALRQQLDLYICLRPVRYYQGTPSPVKQPE 146
                                           ************************************************************************* PP

                             TIGR00183 146 kvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyai 218
                                            +d+vifren+ediyaGiew+++s+ea k+ikfl++e++vkkir+pe++GiGikp+seegtkrlvr+aieyai
  NCBI__GCF_001655005.1:WP_004090093.1 147 LTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLRDEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAI 219
                                           ************************************************************************* PP

                             TIGR00183 219 endkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqilt 291
                                           +nd++s+tlvhkGnimkfteGafkdwGy+la++efg e+i+ ++w k+knp++Gk+i+vkd+iada+lqqil+
  NCBI__GCF_001655005.1:WP_004090093.1 220 TNDRDSLTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWVKIKNPKTGKDIIVKDVIADAFLQQILL 292
                                           ************************************************************************* PP

                             TIGR00183 292 rpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvlll 364
                                           rp+eydvia+mnlnGdy+sdalaa+vGG+GiapGanigde+a+feathGtapkyaG+dkvnpgs+ils++++l
  NCBI__GCF_001655005.1:WP_004090093.1 293 RPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMML 365
                                           ************************************************************************* PP

                             TIGR00183 365 eflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                           +++ w eaadlivk++e aia+k+vtyd++r ++gak +kcsef++ai++++
  NCBI__GCF_001655005.1:WP_004090093.1 366 RHMEWFEAADLIVKGMEGAIAAKTVTYDFERQLEGAKLLKCSEFGDAIIKHM 417
                                           **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (417 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.47
//
[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