Alignments for a candidate for hutU in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Collimonas arenae Ter10

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_061533209.1 CAter10_RS09450 urocanate hydratase

Query= reanno::acidovorax_3H11:Ac3H11_2557
         (574 letters)



>NCBI__GCF_001584165.1:WP_061533209.1
          Length = 567

 Score =  979 bits (2530), Expect = 0.0
 Identities = 472/567 (83%), Positives = 513/567 (90%)

Query: 8   IAAASNTDPRHDASRVIRAPRGSQLTCKSWLTEAAYRMIQNNLDAEVAERPQDLVVYGGI 67
           ++  ++TDPR D SR IRA RG+QLT KSWLTEA  RM+ NNLD EVAERP DLVVYGGI
Sbjct: 1   MSTPTSTDPRRDPSRTIRAARGTQLTAKSWLTEAPLRMLMNNLDPEVAERPNDLVVYGGI 60

Query: 68  GRAARNWECYDQILASLKDLNDDETLLIQSGKPVGVFKTHANAPRVLLANSNLVPKWANW 127
           GRAAR+W C+D+I+ +L  LNDDETLLIQSGKPVGVF+THA+APRVLLANSNLVPKWANW
Sbjct: 61  GRAARDWACFDKIVEALTKLNDDETLLIQSGKPVGVFQTHADAPRVLLANSNLVPKWANW 120

Query: 128 EHFSELDQKGLFMYGQMTAGSWIYIGTQGIVQGTYETFAEAGRKHYGGSLEGKWILTAGL 187
           EHF+ELD+KGLFMYGQMTAGSWIYIG+QGIVQGT+ETFAEAGR+H+GG L G+WILTAGL
Sbjct: 121 EHFNELDRKGLFMYGQMTAGSWIYIGSQGIVQGTFETFAEAGRQHFGGDLSGRWILTAGL 180

Query: 188 GGMGGAQPLAATFAGAVSLNIECQQSSIDFRLRTRYVDKQARDIDHAFELIQQHTAAKEA 247
           GGMGGAQPLAAT AGA SL IEC+QSSIDFRLRTRY+DKQA+++D A +LI+ HT  KEA
Sbjct: 181 GGMGGAQPLAATLAGAASLTIECKQSSIDFRLRTRYLDKQAKNLDDALDLIKYHTERKEA 240

Query: 248 VSIALLGNAAEILPELVRRAKAGGLKPDLVTDQTSAHDLVNGYLPAGWTVAQWRAAQQDV 307
           +SI LLGNAAE+LPELVRRAKAGG+KPDLVTDQTSAHDL+NGYLP GW+V QW AAQ D 
Sbjct: 241 ISIGLLGNAAEVLPELVRRAKAGGIKPDLVTDQTSAHDLINGYLPIGWSVEQWVAAQNDP 300

Query: 308 TQHEVLKKAAAKSCAVHVQAMLDFQHMGIPVVDYGNNIRQVAFDEGVKNAFDFPGFVPAY 367
           +Q   L   AA SCA HVQAMLDF  MGI  VDYGNNIRQVAFD+GVKNAFDFPGFVPAY
Sbjct: 301 SQQARLTADAAHSCAQHVQAMLDFHAMGIKTVDYGNNIRQVAFDQGVKNAFDFPGFVPAY 360

Query: 368 IRPLFCEGKGPFRWVALSGDPEDIRKTDAKIKELFPENKHVHRWLDMAGERIAFQGLPAR 427
           IRPLFCEGKGPFRWVALSGDPEDI KTDAKIKELFPENKHVHRWLDMA ERIAFQGLPAR
Sbjct: 361 IRPLFCEGKGPFRWVALSGDPEDIYKTDAKIKELFPENKHVHRWLDMAHERIAFQGLPAR 420

Query: 428 ICWLGLGERHIAGLAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETEGMKDGTDAVSD 487
           ICWLGLGERHIAGLAFNEMV+NGELKAP+VIGRDHLDTGSVASPNRETE MKDG+DAVSD
Sbjct: 421 ICWLGLGERHIAGLAFNEMVRNGELKAPVVIGRDHLDTGSVASPNRETESMKDGSDAVSD 480

Query: 488 WPLLNALLNTSGGATWVSLHHGGGVGMGYSQHSGMVIVADGTDAAAQRLANVLVNDCGSG 547
           WPLLNALLNTSGGATWVSLHHGGGVGMGYSQH+GMVIVADGTDAAA+RLA VLVNDC SG
Sbjct: 481 WPLLNALLNTSGGATWVSLHHGGGVGMGYSQHAGMVIVADGTDAAAKRLARVLVNDCASG 540

Query: 548 VMRHADAGYELAVETAKKQGLKLPMVK 574
           VMRHADAGYE AVE AK+  L LPM+K
Sbjct: 541 VMRHADAGYEAAVECAKRHNLNLPMIK 567


Lambda     K      H
   0.318    0.134    0.411 

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: 1283
Number of extensions: 56
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: 574
Length of database: 567
Length adjustment: 36
Effective length of query: 538
Effective length of database: 531
Effective search space:   285678
Effective search space used:   285678
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_061533209.1 CAter10_RS09450 (urocanate hydratase)
to HMM TIGR01228 (hutU: urocanate hydratase (EC 4.2.1.49))

# 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/TIGR01228.hmm
# target sequence database:        /tmp/gapView.660853.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01228  [M=545]
Accession:   TIGR01228
Description: hutU: urocanate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.8e-290  947.7   0.6   1.1e-289  947.5   0.6    1.0  1  NCBI__GCF_001584165.1:WP_061533209.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584165.1:WP_061533209.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  947.5   0.6  1.1e-289  1.1e-289       1     545 []      15     565 ..      15     565 .. 0.98

  Alignments for each domain:
  == domain 1  score: 947.5 bits;  conditional E-value: 1.1e-289
                             TIGR01228   1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetll 73 
                                           ++ira+rG++l+ak+w +ea+lr+lmnnldpevae p++lvvyGG+G+aar+w +fdkive l++l+ddetll
  NCBI__GCF_001584165.1:WP_061533209.1  15 RTIRAARGTQLTAKSWLTEAPLRMLMNNLDPEVAERPNDLVVYGGIGRAARDWACFDKIVEALTKLNDDETLL 87 
                                           689********************************************************************** PP

                             TIGR01228  74 vqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlae 146
                                           +qsGkpvgvf+th +aprvl+ansnlvpkwa+we+f+el++kGl myGqmtaGswiyiG+qGi+qGt+et+ae
  NCBI__GCF_001584165.1:WP_061533209.1  88 IQSGKPVGVFQTHADAPRVLLANSNLVPKWANWEHFNELDRKGLFMYGQMTAGSWIYIGSQGIVQGTFETFAE 160
                                           ************************************************************************* PP

                             TIGR01228 147 larkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraee 219
                                           ++r+hfgg+l+g+++ltaGlGgmGGaqpla+tl++a+s+++e++++ id+rl+t+yld+++++ld+al  ++ 
  NCBI__GCF_001584165.1:WP_061533209.1 161 AGRQHFGGDLSGRWILTAGLGGMGGAQPLAATLAGAASLTIECKQSSIDFRLRTRYLDKQAKNLDDALDLIKY 233
                                           ************************************************************************* PP

                             TIGR01228 220 akaeGkalsigllGnaaevleeller....gvvpdvvtdqtsahdellGyipegytvedadklrdeep..eey 286
                                            +++ +a+sigllGnaaevl+el++r    g++pd+vtdqtsahd ++Gy+p g++ve+    +++ +  +  
  NCBI__GCF_001584165.1:WP_061533209.1 234 HTERKEAISIGLLGNAAEVLPELVRRakagGIKPDLVTDQTSAHDLINGYLPIGWSVEQWVAAQNDPSqqARL 306
                                           ************************99666679***************************87776664400445 PP

                             TIGR01228 287 vkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsG 359
                                              a +s a+hv+a+l++   G +t dyGnnirqva+++Gv++afdfpGfvpayir+lfceGkGpfrwvalsG
  NCBI__GCF_001584165.1:WP_061533209.1 307 TADAAHSCAQHVQAMLDFHAMGIKTVDYGNNIRQVAFDQGVKNAFDFPGFVPAYIRPLFCEGKGPFRWVALSG 379
                                           5677889****************************************************************** PP

                             TIGR01228 360 dpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvig 432
                                           dp+diy+td+++kelfpe++++hrw+d+a+e++afqGlparicwlg+ger+ ++la+ne+vr+Gelkapvvig
  NCBI__GCF_001584165.1:WP_061533209.1 380 DPEDIYKTDAKIKELFPENKHVHRWLDMAHERIAFQGLPARICWLGLGERHIAGLAFNEMVRNGELKAPVVIG 452
                                           ************************************************************************* PP

                             TIGR01228 433 rdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdea 505
                                           rdhld+Gsvaspnrete+mkdGsdav+dwpllnallnt +Ga+wvslhhGGGvg+G+s+hag+vivadGtd+a
  NCBI__GCF_001584165.1:WP_061533209.1 453 RDHLDTGSVASPNRETESMKDGSDAVSDWPLLNALLNTSGGATWVSLHHGGGVGMGYSQHAGMVIVADGTDAA 525
                                           ************************************************************************* PP

                             TIGR01228 506 aerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545
                                           a+rl+rvl +d   Gv+rhadaGye a+++ak+++l+lpm
  NCBI__GCF_001584165.1:WP_061533209.1 526 AKRLARVLVNDCASGVMRHADAGYEAAVECAKRHNLNLPM 565
                                           ***************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (567 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: 20.89
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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