Alignments for a candidate for icd in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Thauera aminoaromatica S2

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42); [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) (characterized)
to candidate WP_004310228.1 C665_RS11500 NADP-dependent isocitrate dehydrogenase

Query= BRENDA::P08200
         (416 letters)



>NCBI__GCF_000310185.1:WP_004310228.1
          Length = 414

 Score =  629 bits (1623), Expect = 0.0
 Identities = 308/415 (74%), Positives = 353/415 (85%), Gaps = 3/415 (0%)

Query: 2   ESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGER 61
           ESK+ VPA G+KI        VP+NPIIP+IEGDGIGVD+TP M+KV+DAAV+KAY G++
Sbjct: 3   ESKIKVPAGGQKIVPGQA---VPDNPIIPFIEGDGIGVDITPVMIKVIDAAVDKAYGGKK 59

Query: 62  KISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQE 121
           KI WME+Y GEKSTQ+YG D WLP ET D ++ Y V+IKGP+TTPVGGGIRSLNVALRQE
Sbjct: 60  KIHWMEVYAGEKSTQIYGPDEWLPKETFDALKTYSVSIKGPMTTPVGGGIRSLNVALRQE 119

Query: 122 LDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLRE 181
           LDLY C+RPVRY++G PSP+K PELTDMVIFREN+EDIYAGIEW+A S  A+KVI FL+ 
Sbjct: 120 LDLYQCVRPVRYFKGVPSPLKQPELTDMVIFRENTEDIYAGIEWQALSEGAKKVIDFLQG 179

Query: 182 EMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAF 241
           EMGV+KIRFP   GIGIKP S EGT R+VRAAI YAI NDR SVTLVHKGNIMKFTEG F
Sbjct: 180 EMGVRKIRFPATSGIGIKPVSIEGTTRIVRAAIRYAIDNDRKSVTLVHKGNIMKFTEGLF 239

Query: 242 KDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIAC 301
           +D GY++A+EEFG + IDGGPW K KNP +G+EI++KD IADAFLQQILLRPAEYDVIA 
Sbjct: 240 RDTGYRVAQEEFGAQPIDGGPWCKFKNPKSGREILVKDAIADAFLQQILLRPAEYDVIAT 299

Query: 302 MNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAE 361
           +NLNGDYISDALAAQVGGIGIAPGANI D+ A FEATHGTAPKYAG DKVNPGS+ILSAE
Sbjct: 300 LNLNGDYISDALAAQVGGIGIAPGANISDQYACFEATHGTAPKYAGLDKVNPGSLILSAE 359

Query: 362 MMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
           MMLRH+GW EAADL+++GME AI  K VTYDF RLM+GA  + CSEFGDA+I  M
Sbjct: 360 MMLRHLGWKEAADLVIRGMEAAIADKQVTYDFARLMEGANEVSCSEFGDAMIARM 414


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: 644
Number of extensions: 21
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: 414
Length adjustment: 31
Effective length of query: 385
Effective length of database: 383
Effective search space:   147455
Effective search space used:   147455
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_004310228.1 C665_RS11500 (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.5052.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-220  715.6   0.2   1.1e-219  715.4   0.2    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004310228.1  C665_RS11500 NADP-dependent isoc


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004310228.1  C665_RS11500 NADP-dependent isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  715.4   0.2  1.1e-219  1.1e-219       2     416 ..       3     414 .]       2     414 .] 0.99

  Alignments for each domain:
  == domain 1  score: 715.4 bits;  conditional E-value: 1.1e-219
                                 TIGR00183   2 eekvkppeeGekitlkngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevya 70 
                                               e+k+k+p+ G+ki        vp+npiip+ieGdGiGvdi+p +ikv+daav+kay+g+kki w+evya
  lcl|NCBI__GCF_000310185.1:WP_004310228.1   3 ESKIKVPAGGQKIVPG---QAVPDNPIIPFIEGDGIGVDITPVMIKVIDAAVDKAYGGKKKIHWMEVYA 68 
                                               68999******99754...479*********************************************** PP

                                 TIGR00183  71 GekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvps 139
                                               Gek++++yg +e+lp++t+da+k y+v+ikGp+ttpvGgGirslnvalrqeldly c+rpvry+kgvps
  lcl|NCBI__GCF_000310185.1:WP_004310228.1  69 GEKSTQIYGPDEWLPKETFDALKTYSVSIKGPMTTPVGGGIRSLNVALRQELDLYQCVRPVRYFKGVPS 137
                                               ********************************************************************* PP

                                 TIGR00183 140 pvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkr 208
                                               p+k+pe +d+vifrentediyaGiew++ se+akk+i fl+ e++v+kir+p +sGiGikp+s egt r
  lcl|NCBI__GCF_000310185.1:WP_004310228.1 138 PLKQPELTDMVIFRENTEDIYAGIEWQALSEGAKKVIDFLQGEMGVRKIRFPATSGIGIKPVSIEGTTR 206
                                               ********************************************************************* PP

                                 TIGR00183 209 lvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkivv 277
                                               +vr+ai+yai+nd+ksvtlvhkGnimkfteG f+d Gy++a++efg++ i+ ++w+k knp++G++i+v
  lcl|NCBI__GCF_000310185.1:WP_004310228.1 207 IVRAAIRYAIDNDRKSVTLVHKGNIMKFTEGLFRDTGYRVAQEEFGAQPIDGGPWCKFKNPKSGREILV 275
                                               ********************************************************************* PP

                                 TIGR00183 278 kdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapkya 346
                                               kd iada+lqqil+rp+eydviat+nlnGdy+sdalaa+vGG+GiapGani+d+ a feathGtapkya
  lcl|NCBI__GCF_000310185.1:WP_004310228.1 276 KDAIADAFLQQILLRPAEYDVIATLNLNGDYISDALAAQVGGIGIAPGANISDQYACFEATHGTAPKYA 344
                                               ********************************************************************* PP

                                 TIGR00183 347 GldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaiven 415
                                               Gldkvnpgs+ils++++l++lGwkeaadl+++++e+aia+k+vtyd+arlm+ga+ev csef++a++ +
  lcl|NCBI__GCF_000310185.1:WP_004310228.1 345 GLDKVNPGSLILSAEMMLRHLGWKEAADLVIRGMEAAIADKQVTYDFARLMEGANEVSCSEFGDAMIAR 413
                                               *******************************************************************87 PP

                                 TIGR00183 416 l 416
                                               +
  lcl|NCBI__GCF_000310185.1:WP_004310228.1 414 M 414
                                               6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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: 11.39
//
[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