Alignments for a candidate for nagA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Stenotrophomonas chelatiphaga DSM 21508

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_057509307.1 ABB28_RS14525 N-acetylglucosamine-6-phosphate deacetylase

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



>NCBI__GCF_001431535.1:WP_057509307.1
          Length = 382

 Score =  379 bits (972), Expect = e-109
 Identities = 207/378 (54%), Positives = 251/378 (66%), Gaps = 2/378 (0%)

Query: 1   MPAALINGRVLTESGVVEGKAVLVKDGLILDVIE--AAQTPSDAKPRDLKGGLLVPGFID 58
           M   L N R+L      +  A++++DG IL V+   A Q     +  DL GG L+PGFID
Sbjct: 1   MKQVLRNARMLVGDEFRDDLALVIEDGRILAVLPDAAPQLGQADEQVDLGGGWLLPGFID 60

Query: 59  TQVNGGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIAR 118
            QVNGGGG LFN+ P V T+ TI AAHRRFGTT  LPTLISDDL+V+  A+ AT +AIA+
Sbjct: 61  VQVNGGGGALFNNTPDVATLRTIAAAHRRFGTTALLPTLISDDLQVMRAAIAATHDAIAQ 120

Query: 119 GVPGVLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQI 178
            VPGV+G+H+EGP++ P RKG HD  KFRV D + +AL  SL  G TL+TLAPER   + 
Sbjct: 121 QVPGVIGIHLEGPYIAPARKGTHDVSKFRVPDADEIALAASLDNGVTLLTLAPERVPLET 180

Query: 179 IRRLADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPD 238
           IR L + GVIVAAGHT A Y  +R  L+ G+ GFTHL+NAMSPL  REPGAVGAALE  D
Sbjct: 181 IRALVERGVIVAAGHTAASYEEVRAGLDAGIRGFTHLYNAMSPLQGREPGAVGAALEDRD 240

Query: 239 AWCGIIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVC 298
           +W GIIVDG HV P  L++AL  +   R +LVTDAMP VG  D  + L G  I  VDGV 
Sbjct: 241 SWVGIIVDGVHVHPGSLRVALAAKPRGRLLLVTDAMPPVGADDPSYELYGEIITAVDGVV 300

Query: 299 VDDHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAAD 358
            +  G+LAGS LDM  AVRN + LL   L +A  MAS  PA FL +    G IA G+ AD
Sbjct: 301 RNAAGSLAGSALDMATAVRNTVQLLGQPLAEAARMASTYPARFLNVDDRLGHIAEGFQAD 360

Query: 359 LCLLNDRLEVAATWIDGQ 376
           L LL+D L+V  TWI GQ
Sbjct: 361 LVLLDDALQVRGTWIAGQ 378


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: 470
Number of extensions: 16
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: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
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_057509307.1 ABB28_RS14525 (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.13440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-100  322.9   0.0   1.5e-100  322.8   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509307.1  ABB28_RS14525 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509307.1  ABB28_RS14525 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.8   0.0  1.5e-100  1.5e-100       5     379 ..       3     377 ..       1     378 [. 0.96

  Alignments for each domain:
  == domain 1  score: 322.8 bits;  conditional E-value: 1.5e-100
                                 TIGR00221   5 lllkdkailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdt 71 
                                                +l++ ++l + ++ dd a vi+d+ i av ++a  +  +  +++dl g  l+pG+iDvq+nG+gG+ +
  lcl|NCBI__GCF_001431535.1:WP_057509307.1   3 QVLRNARMLVGDEFRDDLALVIEDGRILAVLPDAAPQlgQADEQVDLGGGWLLPGFIDVQVNGGGGALF 71 
                                               679999**************************98655559999************************** PP

                                 TIGR00221  72 ndasv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslek 139
                                               n++    tl  +  a  + G+t+ Lptli+ + + ++ a+ ++ +++a++    ++G+hleGP++++ +
  lcl|NCBI__GCF_001431535.1:WP_057509307.1  72 NNTPDvATLRTIAAAHRRFGTTALLPTLISDDLQVMRAAIAATHDAIAQQVP-GVIGIHLEGPYIAPAR 139
                                               *96544******************************************9988.9*************** PP

                                 TIGR00221 140 kGahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkea 208
                                               kG+h ++  r pd++    +     + +t +tlap e+++ e i+ l+e g+iv aGht a yee++++
  lcl|NCBI__GCF_001431535.1:WP_057509307.1 140 KGTHDVSKFRVPDADE-IALAASLDNGVTLLTLAP-ERVPLETIRALVERGVIVAAGHTAASYEEVRAG 206
                                               *************987.46666666789*******.99******************************* PP

                                 TIGR00221 209 fkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDs 277
                                                 aGi   thlynams+l++Repg++Ga+L++ d  ++ii+DG+h+hp  +r+a  +k   +l+lvtD+
  lcl|NCBI__GCF_001431535.1:WP_057509307.1 207 LDAGIRGFTHLYNAMSPLQGREPGAVGAALEDRDSWVGIIVDGVHVHPGSLRVALAAKPRGRLLLVTDA 275
                                               ********************************************************************* PP

                                 TIGR00221 278 laaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparal 346
                                               + + ga++ +++  G+ ++  ++ + ++ g laGs+l m  +v+n v   + +l++++r++s +par l
  lcl|NCBI__GCF_001431535.1:WP_057509307.1 276 MPPVGADDPSYELYGEIITAVDGVVRNAAGSLAGSALDMATAVRNTVQLLGQPLAEAARMASTYPARFL 344
                                               ********************************************************************* PP

                                 TIGR00221 347 giddrlGsvakGkdanLavltkdfeviltiveg 379
                                               ++ddrlG +a+G +a+L++l+   +v +t + g
  lcl|NCBI__GCF_001431535.1:WP_057509307.1 345 NVDDRLGHIAEGFQADLVLLDDALQVRGTWIAG 377
                                               *****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (382 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: 11.50
//
[ok]

This GapMind analysis is from Sep 24 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