Aligments for a candidate for icd in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for icd in Herbaspirillum seropedicae SmR1

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate HSERO_RS12570 HSERO_RS12570 isocitrate dehydrogenase

Query= BRENDA::O53611
         (745 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS12570 HSERO_RS12570 isocitrate
           dehydrogenase
          Length = 742

 Score = 1111 bits (2873), Expect = 0.0
 Identities = 546/738 (73%), Positives = 630/738 (85%), Gaps = 1/738 (0%)

Query: 6   PTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQRVP 65
           PTIIYTLTDEAP LAT++ LPIV+ F   AGI +  SDISVAARILAEFP+YLT+EQ+VP
Sbjct: 6   PTIIYTLTDEAPYLATHSLLPIVKKFTAAAGIDVVESDISVAARILAEFPEYLTDEQKVP 65

Query: 66  DNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQEKAIK 125
           DNLA LG LTQ PD NIIKLPNISAS+ QL AAI+ELQ +GY +PDYP +P T++EKA++
Sbjct: 66  DNLAALGALTQSPDANIIKLPNISASILQLQAAIRELQSRGYKLPDYPENPTTEEEKALQ 125

Query: 126 ERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRHGDFYA 185
           +RYA+  GSAVNPVLR+GNSDRRAP AVK YARKHPHSM +WSMASRTHVAHM  GDFYA
Sbjct: 126 KRYAKVTGSAVNPVLREGNSDRRAPNAVKNYARKHPHSMAKWSMASRTHVAHMHGGDFYA 185

Query: 186 GEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQMQDA 245
           GEKS+TLD+A +V+M+L+ KSG+TIVLKP++ L  G++IDSMFMSKKALC +YEEQMQDA
Sbjct: 186 GEKSLTLDKAVDVKMDLVTKSGETIVLKPKISLQAGEIIDSMFMSKKALCAYYEEQMQDA 245

Query: 246 FETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLSDLYSK 305
           FET ++ S+HVKATMMKVSHPIVFGHAVR +YKD F KH +LF ++GVN NNG+S +Y K
Sbjct: 246 FETDLLLSVHVKATMMKVSHPIVFGHAVRTYYKDTFTKHAKLFAEIGVNPNNGMSGVYEK 305

Query: 306 IESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAGGKM 365
           I +LP +++ E++ DL      RP LAMVDSA+GI+N H+P+DVIVDASMPAMIRAGGKM
Sbjct: 306 INTLPDAKKAEVLADLKADEAKRPRLAMVDSAKGITNLHAPNDVIVDASMPAMIRAGGKM 365

Query: 366 YGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAEEYGSH 425
           + A GK +DTKA+ PESTF+RIYQE+INFCKTNG FDPTTMGTVPNVGLMAQ+AEEYGSH
Sbjct: 366 WNAAGKTEDTKALLPESTFARIYQEMINFCKTNGAFDPTTMGTVPNVGLMAQKAEEYGSH 425

Query: 426 DKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARISGM 485
           DKTFEI + GVA IV +  G+VLL +NVE GDIWRMC VKDA +RDWVKLAVTRAR+SGM
Sbjct: 426 DKTFEIAQAGVARIVTL-DGQVLLEQNVEEGDIWRMCQVKDAAVRDWVKLAVTRARLSGM 484

Query: 486 PVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTIAAT 545
           P +FWLDPYRPHE ELIKKV TYLKDHD  G DIQIMSQVR+MRYT ER++RGLDTI+ T
Sbjct: 485 PAVFWLDPYRPHEAELIKKVNTYLKDHDLTGADIQIMSQVRAMRYTLERVIRGLDTISVT 544

Query: 546 GNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWD 605
           GNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGM+ETGAGGSAPKHV+QLV ENHLRWD
Sbjct: 545 GNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVGENHLRWD 604

Query: 606 SLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNRGSQFY 665
           SLGEFLAL    E++GIKTGN +AK+L KTLDAA GKLLDN+KSPS KTGELDNRGS FY
Sbjct: 605 SLGEFLALAVSIEEVGIKTGNSKAKILAKTLDAATGKLLDNNKSPSPKTGELDNRGSHFY 664

Query: 666 LAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYAPDSDM 725
           LA+YWAQELAAQ DD +LA+ FA LA  L +NE  IV EL  VQG+ VDIGGYY PD + 
Sbjct: 665 LALYWAQELAAQKDDAELAKQFAPLAKALAENEQKIVEELNSVQGKQVDIGGYYLPDREK 724

Query: 726 TTAVMRPSKTFNAALEAV 743
           T AVMRPS T N ALE +
Sbjct: 725 TFAVMRPSATLNQALETL 742


Lambda     K      H
   0.317    0.134    0.388 

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: 1513
Number of extensions: 37
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: 745
Length of database: 742
Length adjustment: 40
Effective length of query: 705
Effective length of database: 702
Effective search space:   494910
Effective search space used:   494910
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 (21.7 bits)
S2: 55 (25.8 bits)

Align candidate HSERO_RS12570 HSERO_RS12570 (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.31147.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 1341.9   2.8          0 1341.7   2.8    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS12570  HSERO_RS12570 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS12570  HSERO_RS12570 isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1341.7   2.8         0         0       3     742 ..       3     742 .]       1     742 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1341.7 bits;  conditional E-value: 0
                                  TIGR00178   3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalae 70 
                                                t +++iiytltdeap lat+sllpivk f+a+aGi+v  +dis+a+rilaefpeylt+eqkv+d+la 
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570   3 TGNPTIIYTLTDEAPYLATHSLLPIVKKFTAAAGIDVVESDISVAARILAEFPEYLTDEQKVPDNLAA 70 
                                                7789**************************************************************** PP

                                  TIGR00178  71 lGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnp 138
                                                lG l++ p+aniiklpnisas+ ql+aai+elq++Gy+lpdype+p+t+eek++++ryak+ Gsavnp
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570  71 LGALTQSPDANIIKLPNISASILQLQAAIRELQSRGYKLPDYPENPTTEEEKALQKRYAKVTGSAVNP 138
                                                ******************************************************************** PP

                                  TIGR00178 139 vlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakd 206
                                                vlreGnsdrrap avk+yarkhph+m +ws++s++hvahm+ gdfya+eks++ld+a +vk++l++k+
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 139 VLREGNSDRRAPNAVKNYARKHPHSMAKWSMASRTHVAHMHGGDFYAGEKSLTLDKAVDVKMDLVTKS 206
                                                ******************************************************************** PP

                                  TIGR00178 207 GketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvr 274
                                                G+++vlk+k++l++ge+ids+++skkal++++ee+++da+e+++lls+h+katmmkvs+pivfGh+vr
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 207 GETIVLKPKISLQAGEIIDSMFMSKKALCAYYEEQMQDAFETDLLLSVHVKATMMKVSHPIVFGHAVR 274
                                                ******************************************************************** PP

                                  TIGR00178 275 vfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitn 342
                                                ++ykd+f+kha+l+ ++G++ +nG++ +y ki++lp+akk e+ adl++  ++rp lamvds+kGitn
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 275 TYYKDTFTKHAKLFAEIGVNPNNGMSGVYEKINTLPDAKKAEVLADLKADEAKRPRLAMVDSAKGITN 342
                                                ******************************************************************** PP

                                  TIGR00178 343 lhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvp 410
                                                lh+p dvivdasmpamira+Gkm+++ gk +dtka+ p+s++a++yq++i++ck+nGafdpttmGtvp
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 343 LHAPNDVIVDASMPAMIRAGGKMWNAAGKTEDTKALLPESTFARIYQEMINFCKTNGAFDPTTMGTVP 410
                                                ******************************************************************** PP

                                  TIGR00178 411 nvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtr 478
                                                nvGlmaqkaeeyGshdktfei ++Gv+r+v  +G+vlle++ve+gdiwrmcqvkda ++dwvklavtr
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 411 NVGLMAQKAEEYGSHDKTFEIAQAGVARIVTLDGQVLLEQNVEEGDIWRMCQVKDAAVRDWVKLAVTR 478
                                                ******************************************************************** PP

                                  TIGR00178 479 arlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGn 546
                                                arlsg+pavfwldp+r+h++elikkv++ylkdhd +G diqi+s+v+a+r++ler+ rG dtisvtGn
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 479 ARLSGMPAVFWLDPYRPHEAELIKKVNTYLKDHDLTGADIQIMSQVRAMRYTLERVIRGLDTISVTGN 546
                                                ******************************************************************** PP

                                  TIGR00178 547 vlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaa 614
                                                +lrdyltdlfpi+elGtsakmls+vplmaGGG+fetGaGGsapkhvqql+ enhlrwdslGeflala 
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 547 ILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVGENHLRWDSLGEFLALAV 614
                                                ******************************************************************** PP

                                  TIGR00178 615 slehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkel 682
                                                s+e+v++ktgn+kak+la+tldaatgklld++ksps k+Geldnrgs+fyla ywaqelaaq +d+el
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 615 SIEEVGIKTGNSKAKILAKTLDAATGKLLDNNKSPSPKTGELDNRGSHFYLALYWAQELAAQKDDAEL 682
                                                ******************************************************************** PP

                                  TIGR00178 683 aasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                                a++fa++a+al++ne+kiv+el++vqG+ vd+gGyy pd ++t +v+rpsat+n++le+l
  lcl|FitnessBrowser__HerbieS:HSERO_RS12570 683 AKQFAPLAKALAENEQKIVEELNSVQGKQVDIGGYYLPDREKTFAVMRPSATLNQALETL 742
                                                *********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (742 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 0.01s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 11.05
//
[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 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

GapMind for catabolism of small carbon sources