GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Pseudomonas fluorescens FW300-N2E2

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate Pf6N2E2_288 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288
          Length = 741

 Score = 1210 bits (3130), Expect = 0.0
 Identities = 607/736 (82%), Positives = 665/736 (90%), Gaps = 1/736 (0%)

Query: 5   KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
           KIIYT TDEAPALATYSLLPI++AFT S+ IAVETRDISLAGR++A+FPE L D + ++D
Sbjct: 6   KIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVAD 64

Query: 65  DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
            LAELG LA TP+ANIIKLPNISASVPQL+AAIKELQ QGY LPDYPE   TD EKD +A
Sbjct: 65  HLAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVTTDAEKDARA 124

Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
           RYDK+KGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ADSKSHVAHM  GDFYGS
Sbjct: 125 RYDKVKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGS 184

Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
           EKAALI A GSVKIELIA+DG++TVLK KT+VQAGEI+D +VMSKNALR+FIAAEIEDAK
Sbjct: 185 EKAALIDAAGSVKIELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAK 244

Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
           ++GVLLSVHLKATMMKVSDPIMFGQIV+EFYKDAL KHA+VL+QIGF++NNGIGDLYARI
Sbjct: 245 QKGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARI 304

Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
           K LP  +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW
Sbjct: 305 KALPAEQQAQIEADIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364

Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
           G DG+LHDTKAVIPDRCYA +YQ VIEDCKQHGAFDPTTMGSVPNVGLMA+KAEEYGSHD
Sbjct: 365 GTDGQLHDTKAVIPDRCYATIYQAVIEDCKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHD 424

Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
           KTFQI  DGVVRV+D +G+ LLEQSVEAGDI+RMCQ KDAPIQDWVKLAVNRARA++TPA
Sbjct: 425 KTFQIKVDGVVRVSDSNGRTLLEQSVEAGDIFRMCQTKDAPIQDWVKLAVNRARASDTPA 484

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           +FWLDP RAHD  VI KV+ YLKDYDT+GLDIRI++PV+A +F+LAR REGKDTISVTGN
Sbjct: 485 IFWLDPMRAHDGVVIEKVQTYLKDYDTAGLDIRIMAPVDAMKFTLARTREGKDTISVTGN 544

Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
           VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ LEE +LRWDSL
Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSL 604

Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
           GEFLALAASLEHLG  Y NPKALVLA TLDQATG+ LD NKSP+RKVG IDNRGSHFYL 
Sbjct: 605 GEFLALAASLEHLGVTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVGGIDNRGSHFYLT 664

Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
           L+WAQALAAQ +D  L+AQF  +AK LTDNE KIV EL A QGKPVDI GYY  N +LTS
Sbjct: 665 LFWAQALAAQDDDAALKAQFATLAKTLTDNEEKIVAELNAVQGKPVDIGGYYFANPELTS 724

Query: 725 KAIRPSATFNAALAPL 740
           KA+RPS TFNAA+A L
Sbjct: 725 KAMRPSNTFNAAIAAL 740


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: 1553
Number of extensions: 54
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: 741
Length adjustment: 40
Effective length of query: 701
Effective length of database: 701
Effective search space:   491401
Effective search space used:   491401
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 Pf6N2E2_288 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
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.1162338.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 1377.2   5.5          0 1377.1   5.5    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288  Isocitrate dehydrogenase [NADP] 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288  Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate deh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1377.1   5.5         0         0       5     742 ..       4     740 ..       1     741 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1377.1 bits;  conditional E-value: 0
                                     TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddala 69 
                                                   ++kiiyt tdeap+latysllpiv+af+asa i+vetrdislagrila+fpe+l + + v d+la
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288   4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVADHLA 67 
                                                   59****************************************************86.68****** PP

                                     TIGR00178  70 elGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGs 134
                                                   elG+la tpeaniiklpnisasvpql+aaikelq++Gy+lpdype  +td+ekd +ary+k+kGs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288  68 ELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVTTDAEKDARARYDKVKGS 132
                                                   ***************************************************************** PP

                                     TIGR00178 135 avnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevk 199
                                                   avnpvlreGnsdrrapl+vk+yarkhphkmG+w+adskshvahm++gdfy+sek++l+daa +vk
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 133 AVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGSEKAALIDAAGSVK 197
                                                   ***************************************************************** PP

                                     TIGR00178 200 ieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvs 264
                                                   ielia+dG++tvlk+k+++++ge++d++v+sk+al++f+++eiedak++gvlls+hlkatmmkvs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 198 IELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAKQKGVLLSVHLKATMMKVS 262
                                                   ***************************************************************** PP

                                     TIGR00178 265 dpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerp 329
                                                   dpi+fG++v +fykd++akha++leq+G++ +nG++dlya+i++lpa ++ +iead+++vy+ rp
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 263 DPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARIKALPAEQQAQIEADIQAVYAARP 327
                                                   ***************************************************************** PP

                                     TIGR00178 330 elamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqavied 394
                                                    lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavipd++ya +yqavied
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 328 SLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVIPDRCYATIYQAVIED 392
                                                   ***************************************************************** PP

                                     TIGR00178 395 ckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwr 459
                                                   ck++GafdpttmG+vpnvGlma+kaeeyGshdktf+i+ dGvvrv ds+G  lle++veagdi+r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 393 CKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKVDGVVRVSDSNGRTLLEQSVEAGDIFR 457
                                                   ***************************************************************** PP

                                     TIGR00178 460 mcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspv 524
                                                   mcq kdapiqdwvklav+rar+s+tpa+fwldp rahd  +i+kv++ylkd+dt Gldi+i+ pv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 458 MCQTKDAPIQDWVKLAVNRARASDTPAIFWLDPMRAHDGVVIEKVQTYLKDYDTAGLDIRIMAPV 522
                                                   ***************************************************************** PP

                                     TIGR00178 525 katrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsap 589
                                                   +a++f+l+r r+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplm+GGGlfetGaGGsap
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 523 DAMKFTLARTREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAP 587
                                                   ***************************************************************** PP

                                     TIGR00178 590 khvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvG 654
                                                   khvqql een+lrwdslGeflalaasleh++v+++n+ka vla+tld+atg +ld +kspsrkvG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 588 KHVQQLLEENFLRWDSLGEFLALAASLEHLGVTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVG 652
                                                   ***************************************************************** PP

                                     TIGR00178 655 eldnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyya 719
                                                    +dnrgs+fyl+ +waq+laaq +d+ l+a+fa++a++lt+neekivael+avqG++vd+gGyy+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 653 GIDNRGSHFYLTLFWAQALAAQDDDAALKAQFATLAKTLTDNEEKIVAELNAVQGKPVDIGGYYF 717
                                                   ***************************************************************** PP

                                     TIGR00178 720 pdtdlttkvlrpsatfnaileal 742
                                                   ++ +lt+k++rps+tfna+++al
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 718 ANPELTSKAMRPSNTFNAAIAAL 740
                                                   ********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (741 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: 43.72
//
[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:

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