GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Pseudomonas fluorescens FW300-N2C3

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate AO356_22125 AO356_22125 isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_22125
          Length = 741

 Score = 1212 bits (3135), Expect = 0.0
 Identities = 607/736 (82%), Positives = 666/736 (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  HLAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVSTDAEKDARA 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 A+GVVRV+D +G+ LLEQ+VEAGDI+RMCQ KDAPIQDWVKLAVNRARA++TPA
Sbjct: 425 KTFQIKANGVVRVSDNTGRTLLEQNVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPA 484

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           +FWLDP RAHD  VI KV+ YLKD+DTSGLDIRI+SPV+A +F+L R REGKDTISVTGN
Sbjct: 485 IFWLDPMRAHDGVVIEKVQTYLKDHDTSGLDIRIMSPVDAMKFTLGRTREGKDTISVTGN 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 GEFLALAASLEHLGGTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVGGIDNRGSHFYLT 664

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

Query: 725 KAIRPSATFNAALAPL 740
           KA+RPSATFNAA+A L
Sbjct: 725 KAMRPSATFNAAIAAL 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: 1578
Number of extensions: 55
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 AO356_22125 AO356_22125 (isocitrate dehydrogenase)
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.3740.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 1378.4   4.4          0 1378.2   4.4    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125  AO356_22125 isocitrate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125  AO356_22125 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1378.2   4.4         0         0       5     742 ..       4     740 ..       1     741 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1378.2 bits;  conditional E-value: 0
                                       TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvdda 67 
                                                     ++kiiyt tdeap+latysllpiv+af+asa i+vetrdislagrila+fpe+l + + v d+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125   4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVADH 65 
                                                     59****************************************************86.68**** PP

                                       TIGR00178  68 laelGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryak 130
                                                     laelG+la tpeaniiklpnisasvpql+aaikelq++Gy+lpdype   td+ekd +ary+k
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125  66 LAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVSTDAEKDARARYDK 128
                                                     *************************************************************** PP

                                       TIGR00178 131 ikGsavnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlld 193
                                                     +kGsavnpvlreGnsdrrapl+vk+yarkhphkmG+w+adskshvahm++gdfy+sek++l+d
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 129 VKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGSEKAALID 191
                                                     *************************************************************** PP

                                       TIGR00178 194 aaeevkieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhl 256
                                                     aa +vkielia+dG++tvlk+k+++++ge++d++v+sk+al++f+++eiedak++gvlls+hl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 192 AAGSVKIELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAKQKGVLLSVHL 254
                                                     *************************************************************** PP

                                       TIGR00178 257 katmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeiea 319
                                                     katmmkvsdpi+fG++v +fykd++akha++leq+G++ +nG++dlya+i++lpa ++ +iea
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 255 KATMMKVSDPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARIKALPAEQQAQIEA 317
                                                     *************************************************************** PP

                                       TIGR00178 320 dlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipds 382
                                                     d+++vy+ rp lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavipd+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 318 DIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVIPDR 380
                                                     *************************************************************** PP

                                       TIGR00178 383 syagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGe 445
                                                     +ya +yqaviedck++GafdpttmG+vpnvGlma+kaeeyGshdktf+i+a+Gvvrv d++G 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 381 CYATIYQAVIEDCKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKANGVVRVSDNTGR 443
                                                     *************************************************************** PP

                                       TIGR00178 446 vlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekyl 508
                                                      lle++veagdi+rmcq kdapiqdwvklav+rar+s+tpa+fwldp rahd  +i+kv++yl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 444 TLLEQNVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPAIFWLDPMRAHDGVVIEKVQTYL 506
                                                     *************************************************************** PP

                                       TIGR00178 509 kdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvv 571
                                                     kdhdt+Gldi+i+spv+a++f+l r r+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 507 KDHDTSGLDIRIMSPVDAMKFTLGRTREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIV 569
                                                     *************************************************************** PP

                                       TIGR00178 572 plmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladt 634
                                                     plm+GGGlfetGaGGsapkhvqql een+lrwdslGeflalaasleh++ +++n+ka vla+t
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 570 PLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSLGEFLALAASLEHLGGTYNNPKALVLAKT 632
                                                     *************************************************************** PP

                                       TIGR00178 635 ldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkne 697
                                                     ld+atg +ld +kspsrkvG +dnrgs+fyl+ +waq+laaq +d+ l+a+fas+a++lt+ne
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 633 LDQATGEFLDRNKSPSRKVGGIDNRGSHFYLTLFWAQALAAQDDDAALKAQFASLAKTLTDNE 695
                                                     *************************************************************** PP

                                       TIGR00178 698 ekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                                     ekivael+avqG++vd+gGyy+++ +lt+k++rpsatfna+++al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 696 EKIVAELNAVQGKPVDIGGYYFANPELTSKAMRPSATFNAAIAAL 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 7.92
//
[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