Alignments for a candidate for nagA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Herbaspirillum seropedicae SmR1

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate HSERO_RS22760 HSERO_RS22760 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::BFirm:BPHYT_RS02730
         (367 letters)



>FitnessBrowser__HerbieS:HSERO_RS22760
          Length = 375

 Score =  475 bits (1223), Expect = e-139
 Identities = 236/365 (64%), Positives = 287/365 (78%), Gaps = 4/365 (1%)

Query: 2   LTGNILTTDGWIHGTLEYENGRITALTGE--RADPSTND-APYILPGFIDLHVHGGGGSD 58
           L GN+LT  GW HG++ ++  RI ++ G   R +P   D   YILPGFIDLHVHGGGG D
Sbjct: 7   LHGNVLTPQGWTHGSMVFDQ-RIRSIDGRPLRREPRLIDEGDYILPGFIDLHVHGGGGRD 65

Query: 59  VMEGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVH 118
           VMEGG A++ + R HAR+GTTSLLATTMTAP  EL   +  +  +   R PG ARVLGVH
Sbjct: 66  VMEGGDAVQVLARLHARHGTTSLLATTMTAPLAELEVALKAIRTSTDTRPPGHARVLGVH 125

Query: 119 LEGPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVR 178
           LEGPYINPGKLGAQPD A+ A +++V    S+APIR++T+APE+ GH++++ ++A RG++
Sbjct: 126 LEGPYINPGKLGAQPDFAIEASLEQVDHLNSLAPIRLITIAPEVDGHLKLVCKLAHRGMK 185

Query: 179 VQLGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLH 238
           VQ+GH+ G+YDD VAAL HGA GFTHLFNAMS  HHR PG+VGAALAHA++AE+IPDLLH
Sbjct: 186 VQIGHTDGSYDDGVAALAHGASGFTHLFNAMSGFHHRAPGMVGAALAHAQYAELIPDLLH 245

Query: 239 VHPGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLT 298
           VHPGAIRAALR+IPRL+ VTDST+A GMPDG+Y LG Q V KC GGVRL DGTLAGS LT
Sbjct: 246 VHPGAIRAALRSIPRLFCVTDSTAAAGMPDGDYALGRQVVHKCAGGVRLDDGTLAGSILT 305

Query: 299 MDQALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYV 358
           MDQALRNL+S+G+ +A+ S R S YAADYLG+ DRGR+A G  ADVVV DR+ AL A YV
Sbjct: 306 MDQALRNLISLGMDVAEASLRTSTYAADYLGLADRGRLATGCHADVVVLDRQFALKAVYV 365

Query: 359 EGEAI 363
           EGE I
Sbjct: 366 EGEEI 370


Lambda     K      H
   0.319    0.136    0.399 

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: 481
Number of extensions: 19
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: 367
Length of database: 375
Length adjustment: 30
Effective length of query: 337
Effective length of database: 345
Effective search space:   116265
Effective search space used:   116265
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate HSERO_RS22760 HSERO_RS22760 (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.28489.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
      1e-78  250.9   0.0    1.2e-78  250.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS22760  HSERO_RS22760 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS22760  HSERO_RS22760 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6   0.0   1.2e-78   1.2e-78      38     379 ..      34     367 ..      18     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 1.2e-78
                                  TIGR00221  38 aeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredee 105
                                                ++l+ e + id +g +++pG+iD++++G+gG d+++   ++++++ +  a++G+ts L+t++t++  e
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760  34 RPLRREPRLID-EGDYILPGFIDLHVHGGGGRDVMEG-GDAVQVLARLHARHGTTSLLATTMTAPLAE 99 
                                                55666666666.799*******************975.5899999999******************** PP

                                  TIGR00221 106 ikkavkvareylakekn..akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvt 171
                                                ++ a+k++r      +   a++LG+hleGP++++ k Ga+p ++  e++ e  ++ l+  +  i+ +t
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760 100 LEVALKAIRTSTDTRPPghARVLGVHLEGPYINPGKLGAQP-DFAIEASLEQ-VDHLNSLA-PIRLIT 164
                                                **********999887668********************97.6777888888.67777655.69**** PP

                                  TIGR00221 172 lapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLd 239
                                                +ape +++ +l+ kl++ g+ v++Ght+  y+   +a   G++  thl+nams ++hR pg++Ga+L+
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760 165 IAPEVDGHLKLVCKLAHRGMKVQIGHTDGSYDDGVAALAHGASGFTHLFNAMSGFHHRAPGMVGAALA 232
                                                ******************************************************************** PP

                                  TIGR00221 240 eddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkng 307
                                                +   ++e+i D lh+hp +ir a  l+ + +l  vtDs+aaag++++ +  + + v    +++  ++g
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760 233 H-AQYAELIPDLLHVHPGAIRAA--LRSIPRLFCVTDSTAAAGMPDGDYALGRQVVHKCAGGVRLDDG 297
                                                *.679****************97..567888******************9999999999999999*** PP

                                  TIGR00221 308 tlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevilt 375
                                                tlaGs+ltm ++++nl+  + + ++++   +s ++a  lg+ dr G +a+G  a+++vl+++f ++  
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760 298 TLAGSILTMDQALRNLISLG-MDVAEASLRTSTYAADYLGLADR-GRLATGCHADVVVLDRQFALKAV 363
                                                ******************99.***********************.*********************99 PP

                                  TIGR00221 376 iveg 379
                                                 veg
  lcl|FitnessBrowser__HerbieS:HSERO_RS22760 364 YVEG 367
                                                9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (375 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.81
//
[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