Alignments for a candidate for icd in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Bacteroides thetaiotaomicron VPI-5482

Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 351599 BT2071 isocitrate dehydrogenase [NADP] (NCBI ptt file)

Query= SwissProt::Q9ZH99
         (427 letters)



>FitnessBrowser__Btheta:351599
          Length = 396

 Score =  502 bits (1292), Expect = e-147
 Identities = 255/407 (62%), Positives = 307/407 (75%), Gaps = 18/407 (4%)

Query: 23  KITVNK-AVLEVPDRPIIPFIEGDGIGIDIAPVMKNVVDAAVEKSYAGKRKIEWMEIYAG 81
           KIT+ K   L VPD P++P+I GDG+G ++ P M++VV+AAV+K+Y GKR+IEW E+ AG
Sbjct: 3   KITMQKDGTLSVPDVPVVPYITGDGVGAEVTPSMQSVVNAAVQKAYGGKRRIEWKEVLAG 62

Query: 82  EKATKVYGKDNWLPDETLEAIKEYQVAIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPV 141
           E+A    G  +WLPDET++A +EY + IKGPLTTPVGGGIRSLNVALRQ LDLYVCLRPV
Sbjct: 63  ERAFNETG--SWLPDETMKAFQEYLIGIKGPLTTPVGGGIRSLNVALRQTLDLYVCLRPV 120

Query: 142 RYFTGVPSPVKTPEKVNMVIFRENSEDIYAGIEWPAGSPEAVKLINFLQNEMGVKKIRFP 201
           R++ GV SPVK PEKVNM +FREN+EDIYAGIEW AG+PEA K   FL+NEMGV K+RFP
Sbjct: 121 RWYQGVHSPVKAPEKVNMCVFRENTEDIYAGIEWEAGTPEAEKFYQFLKNEMGVTKVRFP 180

Query: 202 ETAGIGIKPVSKEGTSRLVRRAIQYAIDNDRDSVTLVHKGNIMKFTEGAFKDWGYEVAVK 261
           ET+  G+KPVS+EGT RLVR A QYA+D+   SVTLVHKGNIMKFTEG FK WGYE+A +
Sbjct: 181 ETSSFGVKPVSREGTERLVRAACQYALDHHLPSVTLVHKGNIMKFTEGGFKKWGYELAQR 240

Query: 262 EFGAKPLDGGPWHVFENPKTGQKITIKDVIADAFLQQILLRPAEYSVIATLNLNGDYISD 321
           EFG    DG             ++ IKD IADAFLQ  LL P EYSVIATLNLNGDY+SD
Sbjct: 241 EFGDALADG-------------RLVIKDCIADAFLQNTLLIPEEYSVIATLNLNGDYVSD 287

Query: 322 ALAAEVGGIGIAPGANLSDTVG--LFEATHGTAPKYAGQDKVNPGSLILSAEMMLRYLGW 379
            LAA VGGIGIAPGAN++   G  +FEATHGTAP  AG+D VNP S+ILSA MML YLGW
Sbjct: 288 QLAAMVGGIGIAPGANINYKTGHAIFEATHGTAPNIAGKDVVNPCSIILSAVMMLEYLGW 347

Query: 380 KEAADLVVQGIEGAIESKTVTYDFARLMTGAKEVSTSQFGKAIIKHI 426
           KEAA L+ + +E +      T+D AR M G   +ST+ F + I++ I
Sbjct: 348 KEAAALIEKALEQSFLDARATHDLARFMPGGTSLSTTAFTREIVERI 394


Lambda     K      H
   0.317    0.136    0.396 

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: 532
Number of extensions: 20
Number of successful extensions: 5
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: 427
Length of database: 396
Length adjustment: 31
Effective length of query: 396
Effective length of database: 365
Effective search space:   144540
Effective search space used:   144540
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 351599 BT2071 (isocitrate dehydrogenase [NADP] (NCBI ptt file))
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.27227.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-180  586.4   0.1   3.8e-180  585.1   0.1    1.6  1  lcl|FitnessBrowser__Btheta:351599  BT2071 isocitrate dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351599  BT2071 isocitrate dehydrogenase [NADP] (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.1   0.1  3.8e-180  3.8e-180      12     416 ..       2     394 ..       1     395 [. 0.98

  Alignments for each domain:
  == domain 1  score: 585.1 bits;  conditional E-value: 3.8e-180
                          TIGR00183  12 ekitlk.ngklvvpnnpiipyieGdGiGvdivpaaikvldaavekaykgekkiawfevyaGekayelygeeeylpe 86 
                                        +kit++ +g l vp+ p++pyi GdG+G++++p+++ v++aav+kay+g+++i w+ev aGe+a++ +g  ++lp+
  lcl|FitnessBrowser__Btheta:351599   2 NKITMQkDGTLSVPDVPVVPYITGDGVGAEVTPSMQSVVNAAVQKAYGGKRRIEWKEVLAGERAFNETG--SWLPD 75 
                                        578875379************************************************************..***** PP

                          TIGR00183  87 dtldaikeykvaikGplttpvGgGirslnvalrqeldlyvclrpvryykgvpspvkepekvdlvifrentediyaG 162
                                        +t++a +ey + ikGplttpvGgGirslnvalrq+ldlyvclrpvr+y+gv spvk pekv++ +frentediyaG
  lcl|FitnessBrowser__Btheta:351599  76 ETMKAFQEYLIGIKGPLTTPVGGGIRSLNVALRQTLDLYVCLRPVRWYQGVHSPVKAPEKVNMCVFRENTEDIYAG 151
                                        **************************************************************************** PP

                          TIGR00183 163 iewaegseeakklikflknelkvkkirlpedsGiGikpiseegtkrlvrkaieyaiendkksvtlvhkGnimkfte 238
                                        iew++g+ ea+k+ +flkne++v+k+r+pe+s  G+kp+s+egt+rlvr+a +ya++++  svtlvhkGnimkfte
  lcl|FitnessBrowser__Btheta:351599 152 IEWEAGTPEAEKFYQFLKNEMGVTKVRFPETSSFGVKPVSREGTERLVRAACQYALDHHLPSVTLVHKGNIMKFTE 227
                                        **************************************************************************** PP

                          TIGR00183 239 GafkdwGyelakkefgeevitkalwdklknpeeGkkivvkdriadallqqiltrpdeydviatmnlnGdylsdala 314
                                        G fk+wGyela++efg+ + +            G+ +v+kd iada+lq+ l+ p+ey+viat+nlnGdy+sd la
  lcl|FitnessBrowser__Btheta:351599 228 GGFKKWGYELAQREFGDALAD------------GR-LVIKDCIADAFLQNTLLIPEEYSVIATLNLNGDYVSDQLA 290
                                        ****************98753............65.9*************************************** PP

                          TIGR00183 315 alvGGlGiapGanigdeva..ifeathGtapkyaGldkvnpgsvilsgvllleflGwkeaadlivkalekaiaske 388
                                        a+vGG+GiapGani+++++  ifeathGtap  aG+d vnp+s+ils+v++le+lGwkeaa li kale++  + +
  lcl|FitnessBrowser__Btheta:351599 291 AMVGGIGIAPGANINYKTGhaIFEATHGTAPNIAGKDVVNPCSIILSAVMMLEYLGWKEAAALIEKALEQSFLDAR 366
                                        ****************98777******************************************************* PP

                          TIGR00183 389 vtydlarlmdgakevkcsefaeaivenl 416
                                         t+dlar+m g +++ ++ f+ +ive++
  lcl|FitnessBrowser__Btheta:351599 367 ATHDLARFMPGGTSLSTTAFTREIVERI 394
                                        *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (396 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.67
//
[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