GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Rhodobacter viridis JA737

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_110804640.1 C8J30_RS05115 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::Caulo:CCNA_00452
         (378 letters)



>NCBI__GCF_003217355.1:WP_110804640.1
          Length = 381

 Score =  249 bits (635), Expect = 1e-70
 Identities = 155/361 (42%), Positives = 209/361 (57%), Gaps = 8/361 (2%)

Query: 18  EGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQVNGGGGVLFNDAPTVET 77
           +GKAV+++   I  ++ A+  P  A+  +L GG+L PG ID QVNGGGGV+ + A  +  
Sbjct: 19  DGKAVVLERAQIAAILPASDLPEGARI-ELGGGILAPGLIDLQVNGGGGVMLSGADPLTE 77

Query: 78  IATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPGVLGLHIEGPFLNPKR 137
           IATI AAH R GTTG LPTLI+    +    + A   A+ R VPG LGLH+EGP L+PKR
Sbjct: 78  IATICAAHARLGTTGLLPTLITTSSSLTRSVLAAGVAAVGR-VPGFLGLHLEGPHLDPKR 136

Query: 138 KGIHDAGKFRVIDDEALALLTSLKRG--KTLVTLAPERTTPQIIRRLADAGVIVAAGHTN 195
            G H A   R + ++ L L+   + G    ++T+AP   TP  I RL  AGV VA GH +
Sbjct: 137 PGCHPAQHIRPMTEDDLDLICEARAGLPALMLTVAPASVTPAQITRLTAAGVTVALGHAD 196

Query: 196 ALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCGIIVDGRHVDPVVL 255
             +A  + A   G +  THLFNAMS L +REPG VGAAL  P A  G+I DG HV P   
Sbjct: 197 CSFAEAQAAHAAGASAVTHLFNAMSQLGAREPGLVGAALSLPFA-AGLIADGIHVAPESA 255

Query: 256 KIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVDDHGTLAGSDLDMIGA 315
           ++ALR  A +R  LVTDAM   G     F+L G+ I   +     ++ TLAG+DL +  A
Sbjct: 256 RLALRL-AGERLFLVTDAMAVAGTDLLDFDLAGQRIHRANRSLRTENDTLAGADLSLPEA 314

Query: 316 VRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLLNDRLEVAATWIDG 375
           +R  I++L L  + A+ MA+  PA+ +G   GR  IAP   ADL    +  +V   W  G
Sbjct: 315 IRFCIEVLGLPPEQALAMATARPAALIGSNRGR--IAPSLPADLVHFTEDWQVNRVWQGG 372

Query: 376 Q 376
           +
Sbjct: 373 K 373


Lambda     K      H
   0.321    0.140    0.410 

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: 458
Number of extensions: 18
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: 378
Length of database: 381
Length adjustment: 30
Effective length of query: 348
Effective length of database: 351
Effective search space:   122148
Effective search space used:   122148
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: 50 (23.9 bits)

Align candidate WP_110804640.1 C8J30_RS05115 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

# 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/TIGR00221.hmm
# target sequence database:        /tmp/gapView.2399875.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00221  [M=380]
Accession:   TIGR00221
Description: nagA: N-acetylglucosamine-6-phosphate deacetylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.9e-78  249.4   0.0    3.5e-78  249.1   0.0    1.0  1  NCBI__GCF_003217355.1:WP_110804640.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110804640.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.1   0.0   3.5e-78   3.5e-78       6     374 ..       5     367 ..       2     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 249.1 bits;  conditional E-value: 3.5e-78
                             TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.e 77 
                                           +l+  +++ ++   d +avv++  +i a+ + ++l+e+  +i+l g +l+pGliD+q+nG+gGv+   a    
  NCBI__GCF_003217355.1:WP_110804640.1   5 ILTGARLFDGQTCHDGKAVVLERAQIAAILPASDLPEGA-RIELGGGILAPGLIDLQVNGGGGVMLSGADPlT 76 
                                           56667788888888999*****************98775.79************************9966558 PP

                             TIGR00221  78 tleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyire 150
                                            +  +  a a+ G+t+ Lptlit++    ++ + +  +++++ ++   LGlhleGP+l +++ G hp ++ir+
  NCBI__GCF_003217355.1:WP_110804640.1  77 EIATICAAHARLGTTGLLPTLITTSSSLTRSVLAAGVAAVGRVPG--FLGLHLEGPHLDPKRPGCHPAQHIRP 147
                                           89999999*************************************..************************** PP

                             TIGR00221 151 pdvellkkfldea.gd.vitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlyn 221
                                            + +   ++++ea ++    ++t+ap  ++t   i++l+ ag+ v +Gh++  ++e+++a  aG++ +thl+n
  NCBI__GCF_003217355.1:WP_110804640.1 148 MTEDD-LDLICEArAGlPALMLTVAP-ASVTPAQITRLTAAGVTVALGHADCSFAEAQAAHAAGASAVTHLFN 218
                                           99877.6999998344234567****.7788888899************************************ PP

                             TIGR00221 222 amskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGke 294
                                           ams+l  Repg++Ga+L    + +++iaDG+h+ p+ +rla +l g+ +l lvtD++a ag++l  f  aG+ 
  NCBI__GCF_003217355.1:WP_110804640.1 219 AMSQLGAREPGLVGAALSL-PFAAGLIADGIHVAPESARLALRLAGE-RLFLVTDAMAVAGTDLLDFDLAGQR 289
                                           *****************99.9**************************.************************* PP

                             TIGR00221 295 vyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavlt 367
                                           +  +++ l  +n+tlaG+ l + e+++  +e  +++ ++++ +++  pa  +g  +r G +a    a+L+ +t
  NCBI__GCF_003217355.1:WP_110804640.1 290 IHRANRSLRTENDTLAGADLSLPEAIRFCIEVLGLPPEQALAMATARPAALIGS-NR-GRIAPSLPADLVHFT 360
                                           **************************************************9994.56.*************** PP

                             TIGR00221 368 kdfevil 374
                                           +d++v +
  NCBI__GCF_003217355.1:WP_110804640.1 361 EDWQVNR 367
                                           ****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (381 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: 00:00:00.00
# Mc/sec: 15.48
//
[ok]

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

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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