GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Caldicellulosiruptor hydrothermalis 108

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013403985.1 CALHY_RS10795 aconitate hydratase

Query= BRENDA::P19414
         (778 letters)



>NCBI__GCF_000166355.1:WP_013403985.1
          Length = 643

 Score =  357 bits (917), Expect = e-103
 Identities = 258/720 (35%), Positives = 364/720 (50%), Gaps = 89/720 (12%)

Query: 60  TYAEKILYGHLDDPHGQDIQRGVSYLKLRPDRVACQDATAQMAILQFMSAGLPQV-AKPV 118
           T A+KI+  HL    G+ I      + +R D+   QD+T  MA LQF + G+ +V  K  
Sbjct: 4   TVAQKIIKQHL--VKGEMIPG--KEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRS 59

Query: 119 TVHCDHLIQAQVGGEKDLKRAIDLNKEVYDFLASATAKYNMGFWKPGSGIIHQIVLENYA 178
             + DH    Q G E         N + + ++ +   KY + F KPG+GI HQ+ LE +A
Sbjct: 60  VAYIDHNT-LQTGPE---------NADDHLYIQTVAKKYGIYFSKPGNGICHQVHLERFA 109

Query: 179 FPGALIIGTDSHTPNAGGLGQLAIGVGGADAVDVMAGRPWELKAPKILGVKLTGKMNGWT 238
            PG  ++G+DSHTP AGG+G LAIG GG D    M G  + L  PKI+ V L GK+  W 
Sbjct: 110 VPGQTLLGSDSHTPTAGGIGMLAIGAGGLDVAVAMGGGEYYLIMPKIVKVNLKGKLQPWV 169

Query: 239 SPKDIILKLAGITTVKGGTGKIVEYFGDGVDTFSATGMGTICNMGAEIGATTSVFPFNKS 298
           S KDIIL+L    TVKGG GKI EY G+GV T S     TI NMGAE+GATTS+FP ++ 
Sbjct: 170 SAKDIILELLRRLTVKGGVGKIFEYTGEGVKTLSIPERATITNMGAELGATTSIFPSDEV 229

Query: 299 MIEYLEATGRGKIADFAKLYHKDLLSADKDAEYDEVVEIDLNTLEPYINGPFTPDLATPV 358
             E+L+A GR   ADF ++        D DA+YDE +EIDL++L P    P +PD   PV
Sbjct: 230 TYEFLKAQGRE--ADFVEIL------PDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPV 281

Query: 359 SKMKEVAVANNWPLDVRVGLIGSCTNSSYEDMSRSASIVKDAAAHGLKSKTIFTVTPGSE 418
           S++K + V            IGSCTNSSY+D+ + A I++      +       ++PGS+
Sbjct: 282 SELKGIKVDQ--------VAIGSCTNSSYKDLMKVAKILEGKT---IAEHVSLVISPGSK 330

Query: 419 QIRATIERDGQLETFKEFGGIVLANACGPCIGQWDRRDIKKGDKNTIVSSYNRNFTSRND 478
           Q+ + + ++G L +    G  +L  ACGPCIG               + ++NRNF  R+ 
Sbjct: 331 QVLSMLAQNGALASMVAAGARILECACGPCIGMGQ----APRTNGISLRTFNRNFEGRS- 385

Query: 479 GNPQTHAFVASPELVTAFAIAGDLRFNPLTDKLKDKDGNEFMLKPPHGDGLPQRGYDAGE 538
           G P    ++ SPE   A AI G L  +P T       G+E  ++ P       + +   +
Sbjct: 386 GTPSAQVYLVSPETAAASAITGYLT-DPRT------LGDEPKVEMP-------KSFLVND 431

Query: 539 NTYQAPPADRSTVEVKVSPTSDRLQLLKPFKPWDGKDAKDM---PILIKAVGKTTTDHIS 595
           N    P  +   VEV   P       +KPF    GK   D+    +LIK     TTDHI 
Sbjct: 432 NLIVPPAENPHEVEVIRGPN------IKPFP--QGKPLPDVVVGKVLIKLGDNITTDHIM 483

Query: 596 MA-GPWLKYRGHLENISNNYMIGAINAENKKANCVKNVYTGEYKGVPDTARDYRDQGIKW 654
            +    L YR ++  +S +Y +   +                    PD  +  R+ G  +
Sbjct: 484 PSNAKLLPYRSNIPYLS-DYCLTPCD--------------------PDFPKRARENGGGF 522

Query: 655 VVIGDENFGEGSSREHAALEPRFLGGFAIITKSFARIHETNLKKQGLLPLNFKNPADYDK 714
           +V G  N+G+GSSREHAAL P +LG   ++ KSFARIH  NL   G++P+ F+NP+DYD 
Sbjct: 523 IV-GGVNYGQGSSREHAALVPLYLGIKGVLAKSFARIHMANLINNGIIPMVFENPSDYDT 581

Query: 715 INPDDRIDILGLAELAPGKPVTMRVHPKNGKPWDAVLTHTFNDEQIEWFKYGSALNKIKA 774
           I   D + I    E      V +  +   G  +  +L  T  D Q +   +G  LN  KA
Sbjct: 582 IEEMDELKIENAREQIEKSDVLIIENVTKGLKYKMILNLT--DRQRQMILHGGLLNLTKA 639


Lambda     K      H
   0.317    0.136    0.405 

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: 1133
Number of extensions: 56
Number of successful extensions: 7
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: 778
Length of database: 643
Length adjustment: 39
Effective length of query: 739
Effective length of database: 604
Effective search space:   446356
Effective search space used:   446356
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_013403985.1 CALHY_RS10795 (aconitate hydratase)
to HMM TIGR01342 (putative aconitate hydratase (EC 4.2.1.3))

# 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/TIGR01342.hmm
# target sequence database:        /tmp/gapView.762813.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01342  [M=655]
Accession:   TIGR01342
Description: acon_putative: putative aconitate hydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-296  969.4   0.1   4.6e-296  969.2   0.1    1.0  1  NCBI__GCF_000166355.1:WP_013403985.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013403985.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  969.2   0.1  4.6e-296  4.6e-296       1     647 [.       4     639 ..       4     643 .] 0.99

  Alignments for each domain:
  == domain 1  score: 969.2 bits;  conditional E-value: 4.6e-296
                             TIGR01342   1 tlaekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknad 73 
                                           t+a+ki+++hlv+g++ pg+eiai+idqtl+qd+tgtm yl+fea+++d vkt+ +v yidh+tlqt   nad
  NCBI__GCF_000166355.1:WP_013403985.1   4 TVAQKIIKQHLVKGEMIPGKEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRSVAYIDHNTLQTGPENAD 76 
                                           89*********************************************************************** PP

                             TIGR01342  74 dhkylrsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageay 146
                                           dh y+++vakkygiy+skpgngichqvh+erfa pg+tllgsdshtptagg+g+laigaggldvavam+g+ y
  NCBI__GCF_000166355.1:WP_013403985.1  77 DHLYIQTVAKKYGIYFSKPGNGICHQVHLERFAVPGQTLLGSDSHTPTAGGIGMLAIGAGGLDVAVAMGGGEY 149
                                           ************************************************************************* PP

                             TIGR01342 147 ylkmpkvvnvrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatss 219
                                           yl mpk+v+v+lkgkl  wv+akd+ilellrrl+vkgg+gk++eytgegvk ls+peratitnmgaelgat+s
  NCBI__GCF_000166355.1:WP_013403985.1 150 YLIMPKIVKVNLKGKLQPWVSAKDIILELLRRLTVKGGVGKIFEYTGEGVKTLSIPERATITNMGAELGATTS 222
                                           ************************************************************************* PP

                             TIGR01342 220 ifpsdeitedylaafdreeefvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvg 292
                                           ifpsde+t ++l+a++re +fve+l+d+da+yde+i++dls l pl a p+spdnvvpv e++gikv+qv +g
  NCBI__GCF_000166355.1:WP_013403985.1 223 IFPSDEVTYEFLKAQGREADFVEILPDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPVSELKGIKVDQVAIG 295
                                           ************************************************************************* PP

                             TIGR01342 293 sctnsayvdllraakllegrevskdvvlivapgskqalellaregallellkagvrileaacgacigigfvpa 365
                                           sctns+y+dl++ ak+leg+ + ++v l+++pgskq l +la++gal+ +++ag+rile+acg+cig+g +p 
  NCBI__GCF_000166355.1:WP_013403985.1 296 SCTNSSYKDLMKVAKILEGKTIAEHVSLVISPGSKQVLSMLAQNGALASMVAAGARILECACGPCIGMGQAPR 368
                                           ************************************************************************* PP

                             TIGR01342 366 sdsvslrsfnrnfkgragieddkvylaspevavaaaiageivdprdlaedeglkairvemgekysygdeadid 438
                                           ++++slr+fnrnf+gr+g++ ++vyl+spe+a+a+ai+g + dpr l ++     ++vem++++   d+  ++
  NCBI__GCF_000166355.1:WP_013403985.1 369 TNGISLRTFNRNFEGRSGTPSAQVYLVSPETAAASAITGYLTDPRTLGDE-----PKVEMPKSFLVNDNLIVP 436
                                           ***********************************************986.....899********9998887 PP

                             TIGR01342 439 iltkeeridvelikgpnikslpvkeplgedvegevllkvednittdhiipatadilklrsniealseyvlsrv 511
                                           +   e+  +ve+i+gpnik+ p+ +pl++ v g+vl+k+ dnittdhi+p+ a++l++rsni  ls+y l+  
  NCBI__GCF_000166355.1:WP_013403985.1 437 P--AENPHEVEVIRGPNIKPFPQGKPLPDVVVGKVLIKLGDNITTDHIMPSNAKLLPYRSNIPYLSDYCLTPC 507
                                           5..688899**************************************************************** PP

                             TIGR01342 512 ddefverakkldekgkagvlvagenygqgssrehaalaprflgveavlaksfarihkanlvnfgvlpleidnk 584
                                           d++f +ra++       g +v+g nygqgssrehaal+p +lg++ vlaksfarih anl+n g++p+ ++n 
  NCBI__GCF_000166355.1:WP_013403985.1 508 DPDFPKRARENGG----GFIVGGVNYGQGSSREHAALVPLYLGIKGVLAKSFARIHMANLINNGIIPMVFENP 576
                                           *****99987766....******************************************************** PP

                             TIGR01342 585 edydkielgdevevvdliealkdgeeilvvrktddeeilatldlsevekeiliaggklslikq 647
                                            dyd ie  de+++ +  e++++ +  ++ ++t++ +    l+l+++++++++ gg l+l+k 
  NCBI__GCF_000166355.1:WP_013403985.1 577 SDYDTIEEMDELKIENAREQIEKSDVLIIENVTKGLKYKMILNLTDRQRQMILHGGLLNLTKA 639
                                           ***********************99888899******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (655 nodes)
Target sequences:                          1  (643 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 25.70
//
[ok]

This GapMind analysis is from Sep 24 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