Alignments for a candidate for nagA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Phaeobacter inhibens BS107

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate GFF2745 PGA1_c27880 N-acetylglucosamine-6-phosphate deacetylase NagA

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



>FitnessBrowser__Phaeo:GFF2745
          Length = 386

 Score =  273 bits (697), Expect = 8e-78
 Identities = 160/375 (42%), Positives = 220/375 (58%), Gaps = 4/375 (1%)

Query: 4   ALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQVNG 63
           AL   R+LT  G  +  A++++   I  V+   + P  A+  +L GG+L  GF+D QVNG
Sbjct: 10  ALTGARILTPVGWEDDFALVLRGDQIAAVLPMGKLPEGAELTELDGGILTAGFVDLQVNG 69

Query: 64  GGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPGV 123
           GGGV+FNDAP +E +  I AAH + G T  LPTLI+D    V +A+ AT EAIA GVPG+
Sbjct: 70  GGGVMFNDAPDLEQLQVIAAAHAKIGATSILPTLITDTPNFVARAIEATVEAIAAGVPGI 129

Query: 124 LGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTL--VTLAPERTTPQIIRR 181
           +GLH+EGP L   RKG HDA   R + +  L +L +      +  VTLA E  TP  IR+
Sbjct: 130 IGLHLEGPHLAVSRKGAHDASLIRPMSETDLEMLCAAASRLPVLKVTLACEAATPAQIRQ 189

Query: 182 LADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWC 241
           L++AGV+V+ GHT+A +A    A+  G    THLFNA S L +REPG VGAAL+      
Sbjct: 190 LSEAGVLVSLGHTDASHADCVAAVAAGARCVTHLFNAQSQLGNREPGVVGAALDLGGLSA 249

Query: 242 GIIVDGRHVDPVVLKIALRTR-ALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVD 300
           G+I DG HV P  ++ AL  +    +  LV+D+M T G     F L GR+IR  D     
Sbjct: 250 GLIADGVHVHPASIRAALAAKTGPGQVFLVSDSMATGGSDIDHFTLNGREIRRYDNRLTL 309

Query: 301 DHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLC 360
             GTLAG+ L++  AV+  ++  +++L+ A+ MAS  PA  +G     G + PG  AD+ 
Sbjct: 310 ADGTLAGAHLELATAVKTLVEGCEVALETALEMASARPADLIGRS-DLGRLHPGARADVL 368

Query: 361 LLNDRLEVAATWIDG 375
            LND LE+   W  G
Sbjct: 369 HLNDALELQQVWQSG 383


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: 450
Number of extensions: 19
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: 378
Length of database: 386
Length adjustment: 30
Effective length of query: 348
Effective length of database: 356
Effective search space:   123888
Effective search space used:   123888
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 GFF2745 PGA1_c27880 (N-acetylglucosamine-6-phosphate deacetylase NagA)
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.10430.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.4e-89  285.0   0.0    5.8e-89  284.6   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2745  PGA1_c27880 N-acetylglucosamine-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2745  PGA1_c27880 N-acetylglucosamine-6-phosphate deacetylase NagA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.6   0.0   5.8e-89   5.8e-89       6     372 ..      10     376 ..       7     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 284.6 bits;  conditional E-value: 5.8e-89
                          TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etle 80 
                                        +l+  +ilt     dd+a v+++++i av +  +l+e+ +  +l+g +lt+G++D+q+nG+gGv++nda   e l+
  lcl|FitnessBrowser__Phaeo:GFF2745  10 ALTGARILTPVGWEDDFALVLRGDQIAAVLPMGKLPEGAELTELDGGILTAGFVDLQVNGGGGVMFNDAPDlEQLQ 85 
                                        67888999999999******************************************************8777**** PP

                          TIGR00221  81 imsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvell 156
                                        ++  a ak G+ts Lptlit   + + +a++++ e++a+     i+GlhleGP+l++ +kGah  + ir+ +    
  lcl|FitnessBrowser__Phaeo:GFF2745  86 VIAAAHAKIGATSILPTLITDTPNFVARAIEATVEAIAAGVP-GIIGLHLEGPHLAVSRKGAHDASLIRPMSETD- 159
                                        **************************************9988.8*************************976544. PP

                          TIGR00221 157 kkfldeagd..vitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRe 230
                                         ++l++a+    + kvtla  e  t   i++l eag+ vs+Ght+a  +   +a+ aG+  +thl+na s+l +Re
  lcl|FitnessBrowser__Phaeo:GFF2745 160 LEMLCAAASrlPVLKVTLAC-EAATPAQIRQLSEAGVLVSLGHTDASHADCVAAVAAGARCVTHLFNAQSQLGNRE 234
                                        388999998555789*****.66677789*********************************************** PP

                          TIGR00221 231 pgviGavLdeddvvteiiaDGlhihpknirlakklk.gdsklvlvtDslaaagaklekfifaGkevyiredtlldk 305
                                        pgv+Ga+Ld +++++++iaDG+h+hp+ ir a  +k g  ++ lv Ds+a+ g ++++f+ +G+e+   +++l  +
  lcl|FitnessBrowser__Phaeo:GFF2745 235 PGVVGAALDLGGLSAGLIADGVHVHPASIRAALAAKtGPGQVFLVSDSMATGGSDIDHFTLNGREIRRYDNRLTLA 310
                                        ********************************999956789*********************************** PP

                          TIGR00221 306 ngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfev 372
                                        +gtlaG+ l +  +vk lve +e++l+ +++++s  pa  +g  d  G +  G  a++  l+   e+
  lcl|FitnessBrowser__Phaeo:GFF2745 311 DGTLAGAHLELATAVKTLVEGCEVALETALEMASARPADLIGRSDL-GRLHPGARADVLHLNDALEL 376
                                        ******************************************9997.*********99887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (386 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: 00:00:00.01
# Mc/sec: 11.40
//
[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, or view the source code.

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