Alignments for a candidate for icd in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Cupriavidus basilensis 4G11

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate RR42_RS17135 RR42_RS17135 isocitrate dehydrogenase

Query= SwissProt::Q02NB5
         (418 letters)



>FitnessBrowser__Cup4G11:RR42_RS17135
          Length = 416

 Score =  657 bits (1696), Expect = 0.0
 Identities = 319/416 (76%), Positives = 367/416 (88%), Gaps = 1/416 (0%)

Query: 3   YQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYKGE 62
           YQ I+VPA G+KITVN D SL+VP NPIIPFIEGDG G+DI+PVMIKVVDAAV KAY G+
Sbjct: 2   YQHIKVPA-GEKITVNQDFSLNVPDNPIIPFIEGDGTGLDITPVMIKVVDAAVAKAYGGK 60

Query: 63  RKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVALRQ 122
           RKI+WME+YAGEK+T+VY  D WLP+ETL+ ++DYVVSIKGPLTTPVGGGIRSLNVALRQ
Sbjct: 61  RKISWMEIYAGEKSTKVYGPDVWLPEETLEVLKDYVVSIKGPLTTPVGGGIRSLNVALRQ 120

Query: 123 QLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKFLT 182
           QLDLYVC RPV +F+GVPSPV++P  +DMVIFRENSEDIYAG+EW+A S +A+K+I FL 
Sbjct: 121 QLDLYVCLRPVAYFKGVPSPVREPQKIDMVIFRENSEDIYAGIEWEAESDQAKKLIAFLQ 180

Query: 183 EEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTEGA 242
            EMGVKKIRF +  GIG+KPVS++GTKRLVRKA+QYA+DND+ SVT+VHKGNIMKFTEG 
Sbjct: 181 NEMGVKKIRFPDTSGIGVKPVSKQGTKRLVRKAIQYAIDNDKPSVTIVHKGNIMKFTEGG 240

Query: 243 FKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDVIA 302
           F+DW YE+A+ EFGAEL+DGGPW +FKNPKTG+ +V+KD IADA LQQILLRPAEY VIA
Sbjct: 241 FRDWAYELAQQEFGAELIDGGPWCKFKNPKTGREIVIKDAIADAFLQQILLRPAEYSVIA 300

Query: 303 TLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLILSA 362
           TLNLNGDY+SDALAA+VGGIGIAPGANLSDSVAMFEATHGTAPKYAG+D VNPGS ILSA
Sbjct: 301 TLNLNGDYISDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKYAGKDYVNPGSEILSA 360

Query: 363 EMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM 418
           EMMLRHMGWTEAADLII     +I +K VTYDF RL++GAT +SCS FG  MI  M
Sbjct: 361 EMMLRHMGWTEAADLIISSMEKSILSKKVTYDFARLLEGATQVSCSGFGQVMIDNM 416


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: 671
Number of extensions: 23
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: 416
Length adjustment: 31
Effective length of query: 387
Effective length of database: 385
Effective search space:   148995
Effective search space used:   148995
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 RR42_RS17135 RR42_RS17135 (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.689.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-225  734.7   0.4   1.5e-225  734.6   0.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS17135  RR42_RS17135 isocitrate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS17135  RR42_RS17135 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.6   0.4  1.5e-225  1.5e-225       2     416 ..       2     416 .]       1     416 [] 0.98

  Alignments for each domain:
  == domain 1  score: 734.6 bits;  conditional E-value: 1.5e-225
                                 TIGR00183   2 eekvkppeeGekitlkng.klvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevy 69 
                                               ++++k+p  Gekit++++  l+vp+npiip+ieGdG+G di+p +ikv+daav+kay+g++ki+w+e+y
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135   2 YQHIKVP-AGEKITVNQDfSLNVPDNPIIPFIEGDGTGLDITPVMIKVVDAAVAKAYGGKRKISWMEIY 69 
                                               5566655.69****9765389************************************************ PP

                                 TIGR00183  70 aGekayelygeeeylpedtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvp 138
                                               aGek++++yg + +lpe+tl+++k+y v+ikGplttpvGgGirslnvalrq+ldlyvclrpv y+kgvp
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135  70 AGEKSTKVYGPDVWLPEETLEVLKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVAYFKGVP 138
                                               ********************************************************************* PP

                                 TIGR00183 139 spvkepekvdlvifrentediyaGiewaegseeakklikflknelkvkkirlpedsGiGikpiseegtk 207
                                               spv+ep+k+d+vifren+ediyaGiew+++s++akkli+fl+ne++vkkir+p++sGiG+kp+s++gtk
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135 139 SPVREPQKIDMVIFRENSEDIYAGIEWEAESDQAKKLIAFLQNEMGVKKIRFPDTSGIGVKPVSKQGTK 207
                                               ********************************************************************* PP

                                 TIGR00183 208 rlvrkaieyaiendkksvtlvhkGnimkfteGafkdwGyelakkefgeevitkalwdklknpeeGkkiv 276
                                               rlvrkai+yai+ndk svt+vhkGnimkfteG f+dw yela++efg+e+i+ ++w+k knp++G++iv
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135 208 RLVRKAIQYAIDNDKPSVTIVHKGNIMKFTEGGFRDWAYELAQQEFGAELIDGGPWCKFKNPKTGREIV 276
                                               ********************************************************************* PP

                                 TIGR00183 277 vkdriadallqqiltrpdeydviatmnlnGdylsdalaalvGGlGiapGanigdevaifeathGtapky 345
                                               +kd iada+lqqil+rp+ey+viat+nlnGdy+sdalaa+vGG+GiapGan++d+va+feathGtapky
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135 277 IKDAIADAFLQQILLRPAEYSVIATLNLNGDYISDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKY 345
                                               ********************************************************************* PP

                                 TIGR00183 346 aGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaskevtydlarlmdgakevkcsefaeaive 414
                                               aG+d vnpgs ils++++l+++Gw+eaadli++++ek+i sk+vtyd+arl++ga++v cs f++++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135 346 AGKDYVNPGSEILSAEMMLRHMGWTEAADLIISSMEKSILSKKVTYDFARLLEGATQVSCSGFGQVMID 414
                                               ********************************************************************* PP

                                 TIGR00183 415 nl 416
                                               n+
  lcl|FitnessBrowser__Cup4G11:RR42_RS17135 415 NM 416
                                               98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (416 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.98
//
[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