GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Pedobacter sp. GW460-11-11-14-LB5

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate CA265_RS02350 CA265_RS02350 isocitrate dehydrogenase (NADP(+))

Query= SwissProt::P16100
         (741 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS02350 CA265_RS02350 isocitrate
           dehydrogenase (NADP(+))
          Length = 739

 Score = 1009 bits (2608), Expect = 0.0
 Identities = 503/739 (68%), Positives = 590/739 (79%), Gaps = 2/739 (0%)

Query: 2   STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
           +T KIIYT TDEAP LATYSLLPI++AFT S+GI VETRDISLAGR++A FPEYL D QK
Sbjct: 3   NTSKIIYTKTDEAPMLATYSLLPIVQAFTASAGIDVETRDISLAGRILANFPEYLKDDQK 62

Query: 62  ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
           I D LAELG LATTP+ANIIKLPNISAS+PQL  AI ELQ QG+ +P+YP+  ++D EK 
Sbjct: 63  IGDALAELGALATTPEANIIKLPNISASIPQLVGAITELQSQGFAIPNYPDNAQSDEEKA 122

Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
           +KA+Y K+ GSAVNPVLREGNSDRRAP +VKNYA+++PH MG WSADSK+ VA M  GDF
Sbjct: 123 IKAKYAKVLGSAVNPVLREGNSDRRAPKAVKNYAKQNPHSMGKWSADSKTKVASMTEGDF 182

Query: 182 YGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIE 241
           YGSEK+  +      KIE +A DG+ T LK  + ++AGE+IDSS +S +AL+ F+A EI 
Sbjct: 183 YGSEKSTTVAEASQFKIEFVAADGTVTELKGLSPLKAGEVIDSSALSLSALKTFVAKEIA 242

Query: 242 DAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLY 301
           +AK  GVLLS HLKATMMKVSDPI+FG IV  ++ D  TK+A++ K++  D  NG+GD+Y
Sbjct: 243 EAKAAGVLLSAHLKATMMKVSDPIIFGAIVEVYFADVFTKYADLFKELNIDTRNGLGDVY 302

Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
           A+I     AKQ E+EA +       P LAMVNSDKGITNLHVPSDVIVDASMPAMIR SG
Sbjct: 303 AKIAG--NAKQAEVEAALAQAIENGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSG 360

Query: 362 KMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYG 421
           +MW   GK  DT A+IPDR YAGVY   I+DCK +GAFD TT+GSVPNVGLMAQKAEEYG
Sbjct: 361 QMWNAAGKAQDTIALIPDRSYAGVYTATIDDCKANGAFDVTTIGSVPNVGLMAQKAEEYG 420

Query: 422 SHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATN 481
           SHDKTFQ    G +RVTD  GK+  +Q VE GDI+RMCQ KDAPIQDWVKLAVNR+R + 
Sbjct: 421 SHDKTFQATGSGTIRVTDADGKVFFDQKVEKGDIFRMCQTKDAPIQDWVKLAVNRSRLSE 480

Query: 482 TPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISV 541
           TPAVFWLD  RAHD ++I KV  YLKD+DT+GLDIRIL+P+EAT+F+L RIR+G DTISV
Sbjct: 481 TPAVFWLDENRAHDREIITKVNTYLKDHDTTGLDIRILAPIEATKFTLERIRKGLDTISV 540

Query: 542 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
           TGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKH++QF++EGYLRW
Sbjct: 541 TGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHIEQFIDEGYLRW 600

Query: 602 DSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHF 661
           DSLGEFLAL ASLEHL     N KA VLA  LD+A  K L  +KSP RK+G IDNRGSHF
Sbjct: 601 DSLGEFLALQASLEHLSQTQNNTKAQVLADALDEANAKFLATDKSPGRKLGTIDNRGSHF 660

Query: 662 YLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTD 721
           YLALYWA+ALAAQT+D +LQA+F  +AK L  NE KI  EL  AQGKP +I GYY+PN +
Sbjct: 661 YLALYWAEALAAQTKDADLQARFAPLAKTLFANEAKINEELIGAQGKPQNIGGYYNPNDE 720

Query: 722 LTSKAIRPSATFNAALAPL 740
           L SKA+RPS T N +LA L
Sbjct: 721 LASKAMRPSETLNTSLASL 739


Lambda     K      H
   0.315    0.131    0.374 

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: 1404
Number of extensions: 45
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: 741
Length of database: 739
Length adjustment: 40
Effective length of query: 701
Effective length of database: 699
Effective search space:   489999
Effective search space used:   489999
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 (21.5 bits)
S2: 55 (25.8 bits)

Align candidate CA265_RS02350 CA265_RS02350 (isocitrate dehydrogenase (NADP(+)))
to HMM TIGR00178 (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/TIGR00178.hmm
# target sequence database:        /tmp/gapView.25093.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00178  [M=744]
Accession:   TIGR00178
Description: monomer_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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
          0 1280.4   4.8          0 1280.2   4.8    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS02350  CA265_RS02350 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS02350  CA265_RS02350 isocitrate dehydrogenase (NADP(+))
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1280.2   4.8         0         0       4     741 ..       3     738 ..       1     739 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1280.2 bits;  conditional E-value: 0
                                  TIGR00178   4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalael 71 
                                                +++kiiyt tdeap+latysllpiv+af+asaGi+vetrdislagrila+fpeyl ++qk++dalael
  lcl|FitnessBrowser__Pedo557:CA265_RS02350   3 NTSKIIYTKTDEAPMLATYSLLPIVQAFTASAGIDVETRDISLAGRILANFPEYLKDDQKIGDALAEL 70 
                                                569***************************************************************** PP

                                  TIGR00178  72 GelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpv 139
                                                G la+tpeaniiklpnisas+pql+ ai elq++G+++p+yp+++++deek+ika+yak++Gsavnpv
  lcl|FitnessBrowser__Pedo557:CA265_RS02350  71 GALATTPEANIIKLPNISASIPQLVGAITELQSQGFAIPNYPDNAQSDEEKAIKAKYAKVLGSAVNPV 138
                                                ******************************************************************** PP

                                  TIGR00178 140 lreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdG 207
                                                lreGnsdrrap+avk+ya+++ph+mG+wsadsk++va m++gdfy+seks ++ +a++ kie++a+dG
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 139 LREGNSDRRAPKAVKNYAKQNPHSMGKWSADSKTKVASMTEGDFYGSEKSTTVAEASQFKIEFVAADG 206
                                                ******************************************************************** PP

                                  TIGR00178 208 ketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrv 275
                                                ++t lk   +l++gevidss ls +al+ f+++ei++ak+ gvlls+hlkatmmkvsdpi+fG +v v
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 207 TVTELKGLSPLKAGEVIDSSALSLSALKTFVAKEIAEAKAAGVLLSAHLKATMMKVSDPIIFGAIVEV 274
                                                ******************************************************************** PP

                                  TIGR00178 276 fykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnl 343
                                                +++dvf+k+a+l+++l +d+ nGl+d+yaki+   +ak+ e+ea+l ++ e++p lamv+sdkGitnl
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 275 YFADVFTKYADLFKELNIDTRNGLGDVYAKIA--GNAKQAEVEAALAQAIENGPALAMVNSDKGITNL 340
                                                *******************************8..58999***************************** PP

                                  TIGR00178 344 hvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpn 411
                                                hvpsdvivdasmpamir+sG+m+++ gk +dt a+ipd+syagvy a i+dck nGafd tt+G+vpn
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 341 HVPSDVIVDASMPAMIRTSGQMWNAAGKAQDTIALIPDRSYAGVYTATIDDCKANGAFDVTTIGSVPN 408
                                                ******************************************************************** PP

                                  TIGR00178 412 vGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtra 479
                                                vGlmaqkaeeyGshdktf+    G++rv+d++G+v+++++ve+gdi+rmcq kdapiqdwvklav+r+
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 409 VGLMAQKAEEYGSHDKTFQATGSGTIRVTDADGKVFFDQKVEKGDIFRMCQTKDAPIQDWVKLAVNRS 476
                                                ******************************************************************** PP

                                  TIGR00178 480 rlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnv 547
                                                rls+tpavfwld++rahd+e+i+kv++ylkdhdt+Gldi+il p++at+f+lerir+G dtisvtGnv
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 477 RLSETPAVFWLDENRAHDREIITKVNTYLKDHDTTGLDIRILAPIEATKFTLERIRKGLDTISVTGNV 544
                                                ******************************************************************** PP

                                  TIGR00178 548 lrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaas 615
                                                lrdyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkh++q+ +e++lrwdslGeflal as
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 545 LRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHIEQFIDEGYLRWDSLGEFLALQAS 612
                                                ******************************************************************** PP

                                  TIGR00178 616 lehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkela 683
                                                leh++++++n+ka+vlad+ld+a  k+l ++ksp rk G +dnrgs+fyla ywa++laaqt+d++l+
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 613 LEHLSQTQNNTKAQVLADALDEANAKFLATDKSPGRKLGTIDNRGSHFYLALYWAEALAAQTKDADLQ 680
                                                ******************************************************************** PP

                                  TIGR00178 684 asfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailea 741
                                                a+fa++a++l  ne+ki +el  +qG++ ++gGyy+p+++l++k++rps+t+n+ l++
  lcl|FitnessBrowser__Pedo557:CA265_RS02350 681 ARFAPLAKTLFANEAKINEELIGAQGKPQNIGGYYNPNDELASKAMRPSETLNTSLAS 738
                                                ******************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (739 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.15
//
[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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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