GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Psychromonas ossibalaenae JAMM 0738

Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate WP_019616715.1 G327_RS0120675 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::BAA22834.1
         (378 letters)



>NCBI__GCF_000381745.1:WP_019616715.1
          Length = 377

 Score =  483 bits (1244), Expect = e-141
 Identities = 231/376 (61%), Positives = 299/376 (79%), Gaps = 1/376 (0%)

Query: 1   MYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQL 60
           MYALTNC +YT + VL +HAVI+  DKI+ + P++ L + +  +DL GANL+PGFIDLQL
Sbjct: 1   MYALTNCTVYTTDAVLTEHAVIVEDDKIKNIIPLKQLDAAVEKIDLQGANLTPGFIDLQL 60

Query: 61  NGCGGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPN 120
           NGCGGVMFN  +TAET+ +M  ANLKSGCTS+LPTLITSSDE+M+ A+   R +  +  N
Sbjct: 61  NGCGGVMFNSAVTAETLAVMQTANLKSGCTSYLPTLITSSDEDMKTALQVTRSFINQTEN 120

Query: 121 QSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEK 180
           + LGLHLEGPYL++ +KGIH  ++IR     M+D IC N+D+++KVTLAPEN   E +++
Sbjct: 121 EILGLHLEGPYLSIERKGIHRPEYIRKPQTDMVDLICENADIVSKVTLAPENTPIEVVKQ 180

Query: 181 LVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYA 240
           L ++GIVVS+GHTNATY++A+ + ++G +FATHLFNAMTPM GRE GV+GA+YD  ++YA
Sbjct: 181 LSESGIVVSLGHTNATYAQAKAAIDNGASFATHLFNAMTPMTGREAGVIGAVYDN-DIYA 239

Query: 241 GIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDEN 300
           GII DGFHV Y N+RI+ KI GEKL+LVTDATAPAGA++D F FVG  VYY+DGKC   +
Sbjct: 240 GIIVDGFHVAYENVRISKKIMGEKLILVTDATAPAGADIDKFDFVGTTVYYKDGKCFGAD 299

Query: 301 GTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVF 360
           GTLGGSA+TMIE+++ +V+ VGI L+EA+RMATLYPAKAI V++KLG IK G IANL VF
Sbjct: 300 GTLGGSAVTMIESIEQSVKFVGIELEEAVRMATLYPAKAIAVEDKLGSIKPGKIANLAVF 359

Query: 361 DRDFNVKATVVNGQYE 376
             D+ V  TVVNG Y+
Sbjct: 360 TNDYKVTGTVVNGVYK 375


Lambda     K      H
   0.318    0.135    0.388 

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: 467
Number of extensions: 12
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: 378
Length of database: 377
Length adjustment: 30
Effective length of query: 348
Effective length of database: 347
Effective search space:   120756
Effective search space used:   120756
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: 50 (23.9 bits)

Align candidate WP_019616715.1 G327_RS0120675 (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.3484163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-155  502.5   6.2   4.1e-155  502.3   6.2    1.0  1  NCBI__GCF_000381745.1:WP_019616715.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019616715.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.3   6.2  4.1e-155  4.1e-155       4     379 ..       1     372 [.       1     373 [. 0.99

  Alignments for each domain:
  == domain 1  score: 502.3 bits;  conditional E-value: 4.1e-155
                             TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv 76 
                                           +++l++++++t   vl ++av+++d+kik++++ ++l+  +++idl+g++ltpG+iD+qlnGcgGv++n a +
  NCBI__GCF_000381745.1:WP_019616715.1   1 MYALTNCTVYTTDAVLTEHAVIVEDDKIKNIIPLKQLDAAVEKIDLQGANLTPGFIDLQLNGCGGVMFNSAVT 73 
                                           69********************************************************************777 PP

                             TIGR00221  77 .etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyi 148
                                            etl +m+ a+ ksG+ts+Lptlit +de++k a++v+r ++++ +n +iLGlhleGP+ls+e+kG+h++eyi
  NCBI__GCF_000381745.1:WP_019616715.1  74 aETLAVMQTANLKSGCTSYLPTLITSSDEDMKTALQVTRSFINQTEN-EILGLHLEGPYLSIERKGIHRPEYI 145
                                           7**********************************************.************************* PP

                             TIGR00221 149 repdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlyn 221
                                           r+p+ ++ +++++e++d+++kvtlap e++++e++++l e gi+vs+Ghtnaty+++k+a+  G++fathl+n
  NCBI__GCF_000381745.1:WP_019616715.1 146 RKPQTDM-VDLICENADIVSKVTLAP-ENTPIEVVKQLSESGIVVSLGHTNATYAQAKAAIDNGASFATHLFN 216
                                           *******.******************.99******************************************** PP

                             TIGR00221 222 amskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGke 294
                                           am+++++Re gviGav d+ d++++ii+DG h+ ++n+r+ kk+ g+ kl+lvtD++a+aga+++kf f+G +
  NCBI__GCF_000381745.1:WP_019616715.1 217 AMTPMTGREAGVIGAVYDN-DIYAGIIVDGFHVAYENVRISKKIMGE-KLILVTDATAPAGADIDKFDFVGTT 287
                                           *****************99.***************************.************************* PP

                             TIGR00221 295 vyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavlt 367
                                           vy+++++++ ++gtl Gs++tmie++ + v fv+i l+++vr+++l+pa+a+ ++d+lGs++ Gk+anLav+t
  NCBI__GCF_000381745.1:WP_019616715.1 288 VYYKDGKCFGADGTLGGSAVTMIESIEQSVKFVGIELEEAVRMATLYPAKAIAVEDKLGSIKPGKIANLAVFT 360
                                           ************************************************************************* PP

                             TIGR00221 368 kdfeviltiveg 379
                                           +d++v++t+v+g
  NCBI__GCF_000381745.1:WP_019616715.1 361 NDYKVTGTVVNG 372
                                           **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (377 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: 00:00:00.00
# Mc/sec: 22.27
//
[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