Alignments for a candidate for hutU in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Caulobacter crescentus NA1000

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate CCNA_01008 CCNA_01008 urocanate hydratase

Query= reanno::Korea:Ga0059261_3961
         (556 letters)



>FitnessBrowser__Caulo:CCNA_01008
          Length = 554

 Score =  915 bits (2365), Expect = 0.0
 Identities = 441/552 (79%), Positives = 486/552 (88%), Gaps = 3/552 (0%)

Query: 8   RTDNSRHIKAPTGTELSAKSWLTEAPLRMLMNNLDADVAEAPESLVVYGGIGRAARDWQS 67
           R D +R I+  TG E + KSWLTEA LRMLMNNL  DVAE PE LVVYGGIGRAARDW+S
Sbjct: 3   RRDTTRVIRPATGPERTCKSWLTEAALRMLMNNLHPDVAERPEELVVYGGIGRAARDWES 62

Query: 68  YDRIVDALRALDADQTLLVQSGKPVGVFRTHADAPRVLIANSNLVPHWATWEHFNELDRK 127
           YD+IV+ LR L+ D+TLLVQSGKPVGVFRTHADAPRVLIANSNLVP WA+WEHFNELDRK
Sbjct: 63  YDKIVETLRRLEDDETLLVQSGKPVGVFRTHADAPRVLIANSNLVPRWASWEHFNELDRK 122

Query: 128 GLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGDLSGKWVLTAGLGGMGGAQPL 187
           GLAMYGQMTAGSWIYIG QGIVQGTYETFVE GRQHYGGDLSG+W+LTAGLGGMGGAQPL
Sbjct: 123 GLAMYGQMTAGSWIYIGAQGIVQGTYETFVEMGRQHYGGDLSGRWLLTAGLGGMGGAQPL 182

Query: 188 AATMAGASCLAVECQPSRIEMRLKTRYLDRAANSIDEALEIIRTS---DKPVSVGLLGNA 244
           AA MAGA+CLA+ECQPS IEMRL+T YLDR+ + ++EAL  I  S     P+SVGLLGNA
Sbjct: 183 AAVMAGAACLAIECQPSSIEMRLRTGYLDRSTDKVEEALAWIEESCAAKTPISVGLLGNA 242

Query: 245 AEVLPELVRRGIRPDIVTDQTSAHDPVNGYLPAGWTLDEWFTKRETAPHEVEKAARASMA 304
           AE+LPEL +RG+RPD++TDQTSAHDPVNGYLPAGW+L+ W   R+  P +V +AA+ASMA
Sbjct: 243 AELLPELFKRGVRPDLLTDQTSAHDPVNGYLPAGWSLERWHAMRDQDPPQVAEAAKASMA 302

Query: 305 THVRAMLDFHEMGIPTLDYGNNIRQVAKDEGVENAFAFPGFVPAYIRPLFCRGIGPFRWA 364
            HV+AMLDF   G+PT+DYGNNIRQ+A +EGV NAF FPGFVPAYIRPLFCRG+GPFRWA
Sbjct: 303 AHVKAMLDFQAAGVPTVDYGNNIRQMALEEGVTNAFDFPGFVPAYIRPLFCRGVGPFRWA 362

Query: 365 ALSGNPEDIWKTDRKVKELLPGNHHLHNWLDMAKERIAFQGLPARICWVGLGDRHRLALA 424
           ALSG+PEDI KTD KVKEL+P N HLHNWLDMA ++I FQGLPARICWVGLGDRHRL LA
Sbjct: 363 ALSGDPEDIAKTDAKVKELIPDNPHLHNWLDMAGQKIRFQGLPARICWVGLGDRHRLGLA 422

Query: 425 FNEMVASGELEAPIVIGRDHLDSGSVASPNRETEAMMDGSDAVSDWPLLNALLNTASGAT 484
           FNEMVA GEL+APIVIGRDHLDSGSVASPNRETEAM DGSDAVSDWPLLNALLNTASGAT
Sbjct: 423 FNEMVAKGELKAPIVIGRDHLDSGSVASPNRETEAMRDGSDAVSDWPLLNALLNTASGAT 482

Query: 485 WVSLHHGGGVGMGYSQHSGMVIVADGTPEAAKRLERVLWNDPATGVMRHADAGYEIAKNC 544
           WVSLHHGGGVGMG+SQH+GMVIV DGT  AAKR+ RVLWNDPATGVMRHADAGY+IA  C
Sbjct: 483 WVSLHHGGGVGMGFSQHAGMVIVCDGTEAAAKRVARVLWNDPATGVMRHADAGYDIALAC 542

Query: 545 ATEMGLDLPGIL 556
           A E GLDLPGIL
Sbjct: 543 AREKGLDLPGIL 554


Lambda     K      H
   0.318    0.134    0.416 

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: 1187
Number of extensions: 41
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: 556
Length of database: 554
Length adjustment: 36
Effective length of query: 520
Effective length of database: 518
Effective search space:   269360
Effective search space used:   269360
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: 53 (25.0 bits)

Align candidate CCNA_01008 CCNA_01008 (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.9544.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-293  960.7   0.1   1.3e-293  960.5   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01008  CCNA_01008 urocanate hydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01008  CCNA_01008 urocanate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  960.5   0.1  1.3e-293  1.3e-293       2     544 ..       9     551 ..       8     552 .. 1.00

  Alignments for each domain:
  == domain 1  score: 960.5 bits;  conditional E-value: 1.3e-293
                             TIGR01228   2 eiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllv 74 
                                            ir ++G e ++k+w +eaalr+lmnnl p+vae peelvvyGG+G+aar+we++dkive+l+rleddetllv
  lcl|FitnessBrowser__Caulo:CCNA_01008   9 VIRPATGPERTCKSWLTEAALRMLMNNLHPDVAERPEELVVYGGIGRAARDWESYDKIVETLRRLEDDETLLV 81 
                                           588999******************************************************************* PP

                             TIGR01228  75 qsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlael 147
                                           qsGkpvgvf+th +aprvliansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qGtyet++e+
  lcl|FitnessBrowser__Caulo:CCNA_01008  82 QSGKPVGVFRTHADAPRVLIANSNLVPRWASWEHFNELDRKGLAMYGQMTAGSWIYIGAQGIVQGTYETFVEM 154
                                           ************************************************************************* PP

                             TIGR01228 148 arkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeea 220
                                           +r+h+gg+l+g++ ltaGlGgmGGaqpla+ +++a+++a+e++++ i+ rl+t yld+ td+++eala++ee+
  lcl|FitnessBrowser__Caulo:CCNA_01008 155 GRQHYGGDLSGRWLLTAGLGGMGGAQPLAAVMAGAACLAIECQPSSIEMRLRTGYLDRSTDKVEEALAWIEES 227
                                           ************************************************************************* PP

                             TIGR01228 221 kaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakas 293
                                            a+ +++s+gllGnaae+l+el++rgv+pd++tdqtsahd+++Gy+p+g+++e  + +rd++p ++ +aakas
  lcl|FitnessBrowser__Caulo:CCNA_01008 228 CAAKTPISVGLLGNAAELLPELFKRGVRPDLLTDQTSAHDPVNGYLPAGWSLERWHAMRDQDPPQVAEAAKAS 300
                                           ************************************************************************* PP

                             TIGR01228 294 lakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyr 366
                                           +a+hv+a+l++q +G+ t dyGnnirq+a eeGv +afdfpGfvpayir+lfc+G Gpfrw+alsGdp+di +
  lcl|FitnessBrowser__Caulo:CCNA_01008 301 MAAHVKAMLDFQAAGVPTVDYGNNIRQMALEEGVTNAFDFPGFVPAYIRPLFCRGVGPFRWAALSGDPEDIAK 373
                                           ************************************************************************* PP

                             TIGR01228 367 tdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaG 439
                                           td++vkel+p++ +lh+w+d+a +k++fqGlparicw+g+g+r++l+la+ne+v +Gelkap+vigrdhld+G
  lcl|FitnessBrowser__Caulo:CCNA_01008 374 TDAKVKELIPDNPHLHNWLDMAGQKIRFQGLPARICWVGLGDRHRLGLAFNEMVAKGELKAPIVIGRDHLDSG 446
                                           ************************************************************************* PP

                             TIGR01228 440 svaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrv 512
                                           svaspnreteam+dGsdav+dwpllnallnta+Ga+wvslhhGGGvg+Gfs+hag+viv+dGt++aa+r++rv
  lcl|FitnessBrowser__Caulo:CCNA_01008 447 SVASPNRETEAMRDGSDAVSDWPLLNALLNTASGATWVSLHHGGGVGMGFSQHAGMVIVCDGTEAAAKRVARV 519
                                           ************************************************************************* PP

                             TIGR01228 513 ltadpGlGvirhadaGyesaldvakeqgldlp 544
                                           l +dp +Gv+rhadaGy+ al +a+e+gldlp
  lcl|FitnessBrowser__Caulo:CCNA_01008 520 LWNDPATGVMRHADAGYDIALACAREKGLDLP 551
                                           ******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (554 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.99
//
[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 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