Alignments for a candidate for nagA in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align N-acetylglucosamine 6-phosphate deacetylase (NagA;BSU35010) (EC 3.5.1.25) (characterized)
to candidate WP_078430875.1 BK574_RS14455 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::CAB15506.1
         (396 letters)



>NCBI__GCF_002019605.1:WP_078430875.1
          Length = 399

 Score =  370 bits (951), Expect = e-107
 Identities = 198/388 (51%), Positives = 265/388 (68%), Gaps = 3/388 (0%)

Query: 3   ESLLIKDIAIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKE--IQAPADSVLLPGMI 60
           +SLLIK   + TE+ +I+NGY+ +  GKI  +   + ++  ++   ++   D  ++PG I
Sbjct: 6   KSLLIKGGQVYTEDSIIENGYIKVKGGKIVEIGEWKHQKIDAEYDVVEVAPDDKIIPGFI 65

Query: 61  DIHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAA 120
           DIHIHG  GADTMDA+   L+ M S LP EGTTSFLATT+TQ+   I QA+ N  E   A
Sbjct: 66  DIHIHGVNGADTMDATKDALETMVSSLPREGTTSFLATTMTQKVEAIDQAVTNVGELITA 125

Query: 121 EESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPE 180
            ++S   AE+LGIHLEGPF++ KRAGAQP E I   D+E FKKWQQ + G IK+VTLAPE
Sbjct: 126 GQASGK-AEILGIHLEGPFINAKRAGAQPLEHIIEPDLETFKKWQQLSKGNIKLVTLAPE 184

Query: 181 EDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIG 240
           +   FE+IR+L +  I+AS+GHTDA    ++ A +AGA  +THLYN M   HHREPGV+G
Sbjct: 185 QPGGFEMIRYLVENGIVASIGHTDATYEEVNCAIQAGARGVTHLYNQMRGLHHREPGVVG 244

Query: 241 TALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSV 300
            AL H   + E+IADGIH  P   KLA+  KG++ +ILI+D+MRAK LK G+Y+ GGQ V
Sbjct: 245 AALLHVELMAEIIADGIHVRPEMVKLAYKHKGNTGMILISDAMRAKCLKSGIYDLGGQKV 304

Query: 301 TVRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSV 360
           TV+   A+L DGTLAGSILK+ +  +++  +T C+  D   + S N A+ L I D+KGS+
Sbjct: 305 TVKNGEAVLHDGTLAGSILKLGDALKNIVAYTGCTLKDAIEMASGNPARLLKIDDKKGSL 364

Query: 361 TVGKDADLVIVSSDCEVILTICRGNIAF 388
             GKDAD+VIV+ D EV +T CRG  AF
Sbjct: 365 AEGKDADIVIVNKDLEVTMTFCRGKHAF 392


Lambda     K      H
   0.316    0.132    0.377 

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: 455
Number of extensions: 13
Number of successful extensions: 3
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: 396
Length of database: 399
Length adjustment: 31
Effective length of query: 365
Effective length of database: 368
Effective search space:   134320
Effective search space used:   134320
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_078430875.1 BK574_RS14455 (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.622049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-127  412.0   7.0   1.3e-127  411.8   7.0    1.0  1  NCBI__GCF_002019605.1:WP_078430875.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430875.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.8   7.0  1.3e-127  1.3e-127       3     380 .]       6     389 ..       4     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.8 bits;  conditional E-value: 1.3e-127
                             TIGR00221   3 eslllkdkailtendvlddsavvindekikavvteaele..eeikeidlkg.nvltpGliDvqlnGcgGvdtn 72 
                                           +sll+k  +++te  +++++++ ++++ki ++   ++++   e++ +++     + pG+iD++++G++G+dt+
  NCBI__GCF_002019605.1:WP_078430875.1   6 KSLLIKGGQVYTEDSIIENGYIKVKGGKIVEIGEWKHQKidAEYDVVEVAPdDKIIPGFIDIHIHGVNGADTM 78 
                                           578999**************************876655555999999987669******************** PP

                             TIGR00221  73 dasvetleimsealaksGvtsfLptlitredeeikkavkvareylakekn...akiLGlhleGPflslekkGa 142
                                           da+ ++le m + l+++G+tsfL+t++t++ e i +av ++ e +++ ++   a+iLG+hleGPf++ +++Ga
  NCBI__GCF_002019605.1:WP_078430875.1  79 DATKDALETMVSSLPREGTTSFLATTMTQKVEAIDQAVTNVGELITAGQAsgkAEILGIHLEGPFINAKRAGA 151
                                           ********************************************998877788******************** PP

                             TIGR00221 143 hpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitf 215
                                           +p e+i epd e +kk+++ + + i+ vtlape+ + +e+i+ l+e+gi++s+Ght+atyee++ a++aG+  
  NCBI__GCF_002019605.1:WP_078430875.1 152 QPLEHIIEPDLETFKKWQQLSKGNIKLVTLAPEQPGGFEMIRYLVENGIVASIGHTDATYEEVNCAIQAGARG 224
                                           ************************************************************************* PP

                             TIGR00221 216 athlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekf 288
                                           +thlyn m  l+hRepgv+Ga+L + ++++eiiaDG+h+ p+ ++la k kg++ ++l+ D+++a+++k + +
  NCBI__GCF_002019605.1:WP_078430875.1 225 VTHLYNQMRGLHHREPGVVGAALLHVELMAEIIADGIHVRPEMVKLAYKHKGNTGMILISDAMRAKCLKSGIY 297
                                           ************************************************************************* PP

                             TIGR00221 289 ifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkda 361
                                             +G++v++++++++ ++gtlaGs+l++ +++kn+v +++++l+d+++++s npar l idd++Gs+a+Gkda
  NCBI__GCF_002019605.1:WP_078430875.1 298 DLGGQKVTVKNGEAVLHDGTLAGSILKLGDALKNIVAYTGCTLKDAIEMASGNPARLLKIDDKKGSLAEGKDA 370
                                           ************************************************************************* PP

                             TIGR00221 362 nLavltkdfeviltivegk 380
                                           ++++++kd ev++t ++gk
  NCBI__GCF_002019605.1:WP_078430875.1 371 DIVIVNKDLEVTMTFCRGK 389
                                           *****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (399 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: 00:00:00.00
# Mc/sec: 22.68
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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 2024 update 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