Alignments for a candidate for icd in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Acidovorax sp. GW101-3H11

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate Ac3H11_2377 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2377
          Length = 419

 Score =  640 bits (1652), Expect = 0.0
 Identities = 313/416 (75%), Positives = 362/416 (87%)

Query: 3   YQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYKGE 62
           YQ I VPA G KITVNADMSL+VP  PIIPFIEGDG G+DI+PVMIKVV+AAV KAY G+
Sbjct: 4   YQHIVVPAAGQKITVNADMSLNVPDEPIIPFIEGDGTGLDITPVMIKVVNAAVAKAYGGK 63

Query: 63  RKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVALRQ 122
           +KI WMEVYAGEK+T+VY  D WLP+ETL  +R+YVVSIKGPLTTPVGGGIRSLNVALRQ
Sbjct: 64  KKIHWMEVYAGEKSTKVYGPDVWLPEETLAVLREYVVSIKGPLTTPVGGGIRSLNVALRQ 123

Query: 123 QLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKFLT 182
           +LDLYVC RPV++F+GVPSP+K+P   +MVIFRENSEDIYAG+E++A S +A+K+IKFL 
Sbjct: 124 ELDLYVCLRPVQYFKGVPSPLKEPEKTNMVIFRENSEDIYAGIEFEAESDKAKKLIKFLQ 183

Query: 183 EEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTEGA 242
           +EMGVKKIRF    G+G+KPVS+EGT+RLVRKA+QYA+DND+ SVT+VHKGNIMKFTEG 
Sbjct: 184 DEMGVKKIRFPNTSGLGVKPVSREGTERLVRKAIQYAIDNDKPSVTIVHKGNIMKFTEGG 243

Query: 243 FKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDVIA 302
           F+DW Y +A+ EFGAEL+DGGPW + KNPKTGK++ VKD IADA LQQILLRPAEY V+A
Sbjct: 244 FRDWAYALAQKEFGAELIDGGPWCKLKNPKTGKDITVKDSIADAFLQQILLRPAEYSVVA 303

Query: 303 TLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLILSA 362
           TLNLNGDY+SDALAA+VGGIGIAPGAN+SDSVA FEATHGTAPKYAG+D VNPGS ILSA
Sbjct: 304 TLNLNGDYISDALAAQVGGIGIAPGANMSDSVACFEATHGTAPKYAGKDYVNPGSEILSA 363

Query: 363 EMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           EMMLRHMGWT AA+LII     +IA+K VTYDF RLMDGAT +SCS FG  MI  M
Sbjct: 364 EMMLRHMGWTAAANLIISSLEKSIASKKVTYDFARLMDGATQVSCSGFGQVMIDHM 419


Lambda     K      H
   0.317    0.135    0.397 

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: 661
Number of extensions: 20
Number of successful extensions: 1
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: 418
Length of database: 419
Length adjustment: 32
Effective length of query: 386
Effective length of database: 387
Effective search space:   149382
Effective search space used:   149382
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 Ac3H11_2377 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
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.2052.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   5.3e-223  726.2   0.4   6.1e-223  726.0   0.4    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377  Isocitrate dehydrogenase [NADP] 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377  Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.0   0.4  6.1e-223  6.1e-223       2     416 ..       4     419 .]       3     419 .] 0.99

  Alignments for each domain:
  == domain 1  score: 726.0 bits;  conditional E-value: 6.1e-223
                                        TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekk 62 
                                                      ++++++p+ G+kit++++  l+vp++piip+ieGdG+G di+p +ikv++aav+kay+g+kk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377   4 YQHIVVPAAGQKITVNADmSLNVPDEPIIPFIEGDGTGLDITPVMIKVVNAAVAKAYGGKKK 65 
                                                      678999*********875279***************************************** PP

                                        TIGR00183  63 iawfevyaGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldl 124
                                                      i w+evyaGek++++yg + +lpe+tl +++ey v+ikGplttpvGgGirslnvalrqeldl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377  66 IHWMEVYAGEKSTKVYGPDVWLPEETLAVLREYVVSIKGPLTTPVGGGIRSLNVALRQELDL 127
                                                      ************************************************************** PP

                                        TIGR00183 125 yvclrpvryykgvpspvkepekvdlvifrentediyaGiewaegseeakklikflknelkvk 186
                                                      yvclrpv+y+kgvpsp+kepek+++vifren+ediyaGie++++s++akklikfl++e++vk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377 128 YVCLRPVQYFKGVPSPLKEPEKTNMVIFRENSEDIYAGIEFEAESDKAKKLIKFLQDEMGVK 189
                                                      ************************************************************** PP

                                        TIGR00183 187 kirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyel 248
                                                      kir+p++sG+G+kp+s+egt+rlvrkai+yai+ndk svt+vhkGnimkfteG f+dw y+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377 190 KIRFPNTSGLGVKPVSREGTERLVRKAIQYAIDNDKPSVTIVHKGNIMKFTEGGFRDWAYAL 251
                                                      ************************************************************** PP

                                        TIGR00183 249 akkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmnlnGdyls 310
                                                      a+kefg+e+i+ ++w+klknp++Gk+i vkd+iada+lqqil+rp+ey+v+at+nlnGdy+s
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377 252 AQKEFGAELIDGGPWCKLKNPKTGKDITVKDSIADAFLQQILLRPAEYSVVATLNLNGDYIS 313
                                                      ************************************************************** PP

                                        TIGR00183 311 dalaalvGGlGiapGanigdevaifeathGtapkyaGldkvnpgsvilsgvllleflGwkea 372
                                                      dalaa+vGG+GiapGan++d+va feathGtapkyaG+d vnpgs ils++++l+++Gw+ a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377 314 DALAAQVGGIGIAPGANMSDSVACFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHMGWTAA 375
                                                      ************************************************************** PP

                                        TIGR00183 373 adlivkalekaiaskevtydlarlmdgakevkcsefaeaivenl 416
                                                      a+li+++lek+iask+vtyd+arlmdga++v cs f++++++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2377 376 ANLIISSLEKSIASKKVTYDFARLMDGATQVSCSGFGQVMIDHM 419
                                                      ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (419 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: 10.60
//
[ok]

This GapMind analysis is from Sep 17 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