Alignments for a candidate for icd in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Calditerrivibrio nitroreducens DSM 19672

Align isocitrate dehydrogenase (EC 1.1.1.42) (characterized)
to candidate WP_013450590.1 CALNI_RS02310 NADP-dependent isocitrate dehydrogenase

Query= metacyc::MONOMER-11847
         (741 letters)



>NCBI__GCF_000183405.1:WP_013450590.1
          Length = 741

 Score = 1090 bits (2820), Expect = 0.0
 Identities = 542/740 (73%), Positives = 626/740 (84%), Gaps = 1/740 (0%)

Query: 3   SKSTIIYTKIDEAPALATYSLLPIIQAFTRGTGVDVETRDISLAGRIIANFPENLTEEQR 62
           S   II+TKIDEAPALATYS LPI+QAF +GTG++VE +DISL+GRI+ANFP+ L  EQR
Sbjct: 2   SAKKIIWTKIDEAPALATYSFLPIVQAFFKGTGIEVEEKDISLSGRILANFPDFLKPEQR 61

Query: 63  IPDYLAQLGELALTPEANIIKLPNISASIPQLKAAIKELQEHGYNVPNYPEAPSNDEEKA 122
           IPDYLA+LGEL L PEANIIKLPNISASIPQLKAAIKELQE G+ VP+YPE P   EEKA
Sbjct: 62  IPDYLAELGELVLKPEANIIKLPNISASIPQLKAAIKELQEKGFAVPDYPEDPQTPEEKA 121

Query: 123 IQARYAKVLGSAVNPVLREGNSDRRAPLSVKAYAQKHPHRMAAWSKDSKAHVSHMNEGDF 182
           I ARYAKVLGSAVNPVLR+GNSDRRAP+SVK Y++K+PH+MAAW  ++KAHV+HM +GDF
Sbjct: 122 IHARYAKVLGSAVNPVLRQGNSDRRAPISVKNYSKKNPHKMAAWDPNTKAHVAHMTQGDF 181

Query: 183 YGSEQSVTVPAATTVRIEYVNGANEVTVLKEKTALLAGEVIDTSVMNVRKLRDFYAEQIE 242
           YGSE+SVT+  AT+VR E+V+    + VLKE   L  GEV+D+SVMNV +LR FY E IE
Sbjct: 182 YGSEKSVTIEKATSVRYEFVDKNGNIKVLKENLPLTDGEVLDSSVMNVAELRKFYKEHIE 241

Query: 243 DAKSQGVLLSLHLKATMMKISDPIMFGHAVSVFYKDVFDKHGALLAELGVNVNNGLGDLY 302
           DAK+ G+LLSLHLKATMMK+SDP+MFGHAVSVF++DVF+KH     +L VN NNGLGDLY
Sbjct: 242 DAKNSGLLLSLHLKATMMKVSDPVMFGHAVSVFFEDVFNKHSETFKQLKVNPNNGLGDLY 301

Query: 303 AKIQTLPEDKRAEIEADIMAVYKTRPELAMVDSDKGITNLHVPNDIIIDASMPVVVRDGG 362
            KI+TLPE+KR EIEADIMAVY+ RP+LAMVDSDKGITNLH PNDIIIDASMPVVVRDGG
Sbjct: 302 KKIETLPEEKRKEIEADIMAVYEKRPDLAMVDSDKGITNLHQPNDIIIDASMPVVVRDGG 361

Query: 363 KMWGPDGQLHDCKAVIPDRCYATMYGEIVDDCRKNGAFDPSTIGSVPNVGLMAQKAEEYG 422
           KMW   G+L D KA+IPDR YATMY EI++DC+KNGAFDP+TIGSVPNVGLMA +AEEYG
Sbjct: 362 KMWNRQGKLQDTKAIIPDRSYATMYKEIIEDCKKNGAFDPATIGSVPNVGLMAMQAEEYG 421

Query: 423 SHDKTFTAAGDGVIRVVDAD-GTVLMSQKVETGDIFRMCQAKDAPIRDWVGLAVRRAKAT 481
           SHDKTF A  DGVIR+VD +   V+M QKV+  DIFR CQ KD  I+DWV LAV RA+ +
Sbjct: 422 SHDKTFIAEDDGVIRIVDNNTNQVIMEQKVQKYDIFRSCQTKDIAIKDWVKLAVTRARLS 481

Query: 482 GAPAVFWLDSNRAHDAQIIAKVNEYLKDLDTDGVEIKIMPPVEAMRFTLGRFRAGQDTIS 541
             PAVFWLD NRAHDAQIIAKV +YLK+ DT G+E  I+ P EAMRFTL RFRAG DTIS
Sbjct: 482 NTPAVFWLDKNRAHDAQIIAKVEKYLKEHDTTGLEFHILAPQEAMRFTLKRFRAGLDTIS 541

Query: 542 VTGNVLRDYLTDLFPIIELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQFQKEGYLR 601
           VTGNVLRDYLTDLFPIIELGTSAKMLSIVPL+NGGGLFETGAGGSAPKHVQQF  EGYLR
Sbjct: 542 VTGNVLRDYLTDLFPIIELGTSAKMLSIVPLINGGGLFETGAGGSAPKHVQQFLAEGYLR 601

Query: 602 WDSLGEFSALAASLEHLAQTFGNPKAQVLADTLDQAIGKFLDNQKSPARKVGQIDNRGSH 661
           WDSLGEF+AL ASLEH+A  + + KA+VL++TLD+A+ KFLDN+KSPARKVG+IDNRGSH
Sbjct: 602 WDSLGEFTALCASLEHMANLYNDNKARVLSETLDKAVEKFLDNKKSPARKVGEIDNRGSH 661

Query: 662 FYLALYWAEALAAQDSDAEMKARFAGVASSLAAKEELINAELIAAQGSPVDMGGYYQPDD 721
           FYLALYWAEALA Q  DAE+KA+F  +   L+  E+ IN ELI AQG P D+GGYY+PDD
Sbjct: 662 FYLALYWAEALANQTKDAELKAKFEKIYKQLSENEQKINDELIGAQGKPQDIGGYYRPDD 721

Query: 722 EKTAAAMRPSGTLNAIIDAM 741
           +K + AMRPS TLNAIID++
Sbjct: 722 KKASIAMRPSATLNAIIDSI 741


Lambda     K      H
   0.316    0.133    0.380 

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: 1527
Number of extensions: 64
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 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate WP_013450590.1 CALNI_RS02310 (NADP-dependent 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.3245360.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 1254.3   1.9          0 1254.2   1.9    1.0  1  NCBI__GCF_000183405.1:WP_013450590.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183405.1:WP_013450590.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1254.2   1.9         0         0       2     741 ..       2     740 ..       1     741 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1254.2 bits;  conditional E-value: 0
                             TIGR00178   2 stekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGel 74 
                                           s++  kii+t  deap+latys+lpiv+af + +Gieve +disl+grila+fp++l  eq+++d laelGel
  NCBI__GCF_000183405.1:WP_013450590.1   2 SAK--KIIWTKIDEAPALATYSFLPIVQAFFKGTGIEVEEKDISLSGRILANFPDFLKPEQRIPDYLAELGEL 72 
                                           444..9******************************************************************* PP

                             TIGR00178  75 aktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdr 147
                                              peaniiklpnisas+pqlkaaikelq+kG+++pdype+p+t eek+i+aryak++Gsavnpvlr+Gnsdr
  NCBI__GCF_000183405.1:WP_013450590.1  73 VLKPEANIIKLPNISASIPQLKAAIKELQEKGFAVPDYPEDPQTPEEKAIHARYAKVLGSAVNPVLRQGNSDR 145
                                           ************************************************************************* PP

                             TIGR00178 148 raplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklld 220
                                           rap++vk+y++k+phkm +w  ++k+hvahm++gdfy+seksv++++a++v+ e++ k+G+  vlk++l+l+d
  NCBI__GCF_000183405.1:WP_013450590.1 146 RAPISVKNYSKKNPHKMAAWDPNTKAHVAHMTQGDFYGSEKSVTIEKATSVRYEFVDKNGNIKVLKENLPLTD 218
                                           ************************************************************************* PP

                             TIGR00178 221 gevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGl 293
                                           gev+dssv+    l++f++e+iedak+ g+llslhlkatmmkvsdp++fGh+v+vf++dvf kh+e+++ql +
  NCBI__GCF_000183405.1:WP_013450590.1 219 GEVLDSSVMNVAELRKFYKEHIEDAKNSGLLLSLHLKATMMKVSDPVMFGHAVSVFFEDVFNKHSETFKQLKV 291
                                           ************************************************************************* PP

                             TIGR00178 294 dvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmy 366
                                           + +nGl+dly kie+lp+ k++eiead+ +vye+rp+lamvdsdkGitnlh p d+i+dasmp ++r++Gkm+
  NCBI__GCF_000183405.1:WP_013450590.1 292 NPNNGLGDLYKKIETLPEEKRKEIEADIMAVYEKRPDLAMVDSDKGITNLHQPNDIIIDASMPVVVRDGGKMW 364
                                           ************************************************************************* PP

                             TIGR00178 367 gkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrv 439
                                           +++gkl+dtka+ipd+sya +y+++iedckknGafdp+t+G+vpnvGlma +aeeyGshdktf  e+dGv+r+
  NCBI__GCF_000183405.1:WP_013450590.1 365 NRQGKLQDTKAIIPDRSYATMYKEIIEDCKKNGAFDPATIGSVPNVGLMAMQAEEYGSHDKTFIAEDDGVIRI 437
                                           ************************************************************************* PP

                             TIGR00178 440 vd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdh 511
                                           vd ++ +v++e++v++ di+r cq kd  i+dwvklavtrarls+tpavfwld++rahd+++i+kvekylk+h
  NCBI__GCF_000183405.1:WP_013450590.1 438 VDnNTNQVIMEQKVQKYDIFRSCQTKDIAIKDWVKLAVTRARLSNTPAVFWLDKNRAHDAQIIAKVEKYLKEH 510
                                           *956678999*************************************************************** PP

                             TIGR00178 512 dteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGa 584
                                           dt+Gl+ +il p +a+rf+l+r r G dtisvtGnvlrdyltdlfpi+elGtsakmls+vpl++GGGlfetGa
  NCBI__GCF_000183405.1:WP_013450590.1 511 DTTGLEFHILAPQEAMRFTLKRFRAGLDTISVTGNVLRDYLTDLFPIIELGTSAKMLSIVPLINGGGLFETGA 583
                                           ************************************************************************* PP

                             TIGR00178 585 GGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeld 657
                                           GGsapkhvqq+  e++lrwdslGef al+asleh+a+ ++++ka+vl++tld+a++k+ld++ksp+rkvGe+d
  NCBI__GCF_000183405.1:WP_013450590.1 584 GGSAPKHVQQFLAEGYLRWDSLGEFTALCASLEHMANLYNDNKARVLSETLDKAVEKFLDNKKSPARKVGEID 656
                                           ************************************************************************* PP

                             TIGR00178 658 nrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlr 730
                                           nrgs+fyla ywa++la qt+d+el+a+f  + + l++ne+ki  el  +qG++ d+gGyy pd+++++ ++r
  NCBI__GCF_000183405.1:WP_013450590.1 657 NRGSHFYLALYWAEALANQTKDAELKAKFEKIYKQLSENEQKINDELIGAQGKPQDIGGYYRPDDKKASIAMR 729
                                           ************************************************************************* PP

                             TIGR00178 731 psatfnailea 741
                                           psat+nai+++
  NCBI__GCF_000183405.1:WP_013450590.1 730 PSATLNAIIDS 740
                                           ********997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 33.28
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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