Alignments for a candidate for hmgA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Caulobacter crescentus NA1000

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate CCNA_02615 CCNA_02615 homogentisate 1,2-dioxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5290
         (434 letters)



>FitnessBrowser__Caulo:CCNA_02615
          Length = 425

 Score =  560 bits (1442), Expect = e-164
 Identities = 272/420 (64%), Positives = 321/420 (76%), Gaps = 3/420 (0%)

Query: 9   DLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEARRTWMYRI 68
           DL YQ+GFG+ F +EA PGALPVG+NSPQKVP+GLYAE  SG+AFT  R E RRTW+YR+
Sbjct: 2   DLRYQTGFGSYFETEAHPGALPVGRNSPQKVPFGLYAEQLSGSAFTAPRHENRRTWLYRL 61

Query: 69  RPSANHPAFTRLER-QLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAANAGADKP 127
           RPSA H A+    + +L     G  TPNRLRW+PLEIPA PTDF+DGLV +A NA A   
Sbjct: 62  RPSAGHEAYQPYAQDKLVSAFPGPATPNRLRWSPLEIPAAPTDFVDGLVSLAGNADAATL 121

Query: 128 AGISLYQYQANRSME-RVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVLPRGLKF 186
            GI+ + Y  N SM+ RVF+NADGE LIVPQ+G L + TE+GVL+  P  I V+PRG++F
Sbjct: 122 GGIAAHVYLVNVSMKNRVFYNADGEMLIVPQMGELTLVTEMGVLKAGPGHIAVIPRGVRF 181

Query: 187 RIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPTSLVQKF 246
           R+E+  P ARGY+ EN+GA  RLP+LGPIG+NGLANPRDF  PVA +E++  PT ++QKF
Sbjct: 182 RVEVEGP-ARGYVCENYGAAFRLPELGPIGANGLANPRDFEAPVAAFEDIDTPTQVIQKF 240

Query: 247 LGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHG 306
            G LW    DHSPLDVVAWHGN  PY+YDL RFNTI TVS+DHPDPSIFTVLTSP+   G
Sbjct: 241 QGALWAATWDHSPLDVVAWHGNLTPYRYDLSRFNTINTVSYDHPDPSIFTVLTSPSDTPG 300

Query: 307 LANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGASLHSCMS 366
            AN DFVIFPPRWMVAE+TFRPPWFHRN+M+EFMGLI GAYDAKA GF+PGGASLH+CMS
Sbjct: 301 TANCDFVIFPPRWMVAEDTFRPPWFHRNVMSEFMGLIHGAYDAKAGGFVPGGASLHNCMS 360

Query: 367 AHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDACWASLP 426
            HGPD  +  KA    L P KID TMAFMFE+  V RP+  AL+   LQ+DYDACW   P
Sbjct: 361 DHGPDVASHKKATEVVLAPHKIDGTMAFMFESRWVFRPTHLALESAALQSDYDACWTGFP 420


Lambda     K      H
   0.321    0.138    0.435 

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: 746
Number of extensions: 28
Number of successful extensions: 4
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: 434
Length of database: 425
Length adjustment: 32
Effective length of query: 402
Effective length of database: 393
Effective search space:   157986
Effective search space used:   157986
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_02615 CCNA_02615 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

# 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/TIGR01015.hmm
# target sequence database:        /tmp/gapView.20167.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01015  [M=429]
Accession:   TIGR01015
Description: hmgA: homogentisate 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-228  744.8   0.1   1.5e-228  744.6   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02615  CCNA_02615 homogentisate 1,2-dio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02615  CCNA_02615 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  744.6   0.1  1.5e-228  1.5e-228       1     428 [.       2     422 ..       2     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 744.6 bits;  conditional E-value: 1.5e-228
                             TIGR01015   1 elkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelk 73 
                                           +l+y++Gfg++fe+ea+pgalPvG+nsPqk+p+glyaeqlsGsaftaPr+en+r+wlyr+rPsa hea+++++
  lcl|FitnessBrowser__Caulo:CCNA_02615   2 DLRYQTGFGSYFETEAHPGALPVGRNSPQKVPFGLYAEQLSGSAFTAPRHENRRTWLYRLRPSAGHEAYQPYA 74 
                                           589*********************************************************************9 PP

                             TIGR01015  74 eseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfyna 146
                                             ++kl+++f + a+ pn+lrwspleip+ + +dfv+glv+lag++da++  G+a+h+y+vn+sm+++vfyna
  lcl|FitnessBrowser__Caulo:CCNA_02615  75 --QDKLVSAFPGPAT-PNRLRWSPLEIPA-APTDFVDGLVSLAGNADAATLGGIAAHVYLVNVSMKNRVFYNA 143
                                           ..79999****8776.************6.99***************************************** PP

                             TIGR01015 147 dGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveeearGyilevygakfqlPdlGPiGanglan 219
                                           dG++livpq+G+l+++te+G+lk+ P++iaviprGvrfrveve++arGy++e+yga+f+lP+lGPiGanglan
  lcl|FitnessBrowser__Caulo:CCNA_02615 144 DGEMLIVPQMGELTLVTEMGVLKAGPGHIAVIPRGVRFRVEVEGPARGYVCENYGAAFRLPELGPIGANGLAN 216
                                           ************************************************************************* PP

                             TIGR01015 220 prdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPs 292
                                           prdfeaPvaafed ++  +++vi+kfqg+l+aa++dhspldvvawhGn++Py+ydl++fn+in+vs+dhpdPs
  lcl|FitnessBrowser__Caulo:CCNA_02615 217 PRDFEAPVAAFEDIDT--PTQVIQKFQGALWAATWDHSPLDVVAWHGNLTPYRYDLSRFNTINTVSYDHPDPS 287
                                           ****************..88***************************************************** PP

                             TIGR01015 293 iftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnims 365
                                           iftvlt+psd++Gta++dfvifpPrw+vae+tfrPP++hrnvmsefmGli+G+ydak++GfvpgGaslhn+ms
  lcl|FitnessBrowser__Caulo:CCNA_02615 288 IFTVLTSPSDTPGTANCDFVIFPPRWMVAEDTFRPPWFHRNVMSEFMGLIHGAYDAKAGGFVPGGASLHNCMS 360
                                           ************************************************************************* PP

                             TIGR01015 366 ahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428
                                           +hGPdv++++ka+++ l+P+kid  t+afmfes+++++ t+la e+++l++dy+++w+g+ k+
  lcl|FitnessBrowser__Caulo:CCNA_02615 361 DHGPDVASHKKATEVVLAPHKIDG-TMAFMFESRWVFRPTHLALESAALQSDYDACWTGFPKA 422
                                           **********************87.**********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (425 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: 9.38
//
[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