Alignments for a candidate for nagA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Shewanella amazonensis SB2B

Align N-acetylgalactosamine-6-phosphate deacetylase; GalNAc-6-P deacetylase; N-acetylglucosamine-6-phosphate deacetylase; GlcNAc-6-P deacetylase; EC 3.5.1.-; EC 3.5.1.25 (characterized)
to candidate 6937024 Sama_1198 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)

Query= SwissProt::A0KYQ5
         (394 letters)



>FitnessBrowser__SB2B:6937024
          Length = 411

 Score =  360 bits (924), Expect = e-104
 Identities = 199/386 (51%), Positives = 245/386 (63%), Gaps = 5/386 (1%)

Query: 4   NTDFMLIA--DGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTLV 61
           N +F+L+   D ++    GN       +V   I  G   TIS     D P YRL  G L 
Sbjct: 19  NPEFVLVGADDASEFGVTGNAIAALVPDVWLKISQGHIETISRRPDVDLPQYRLP-GILA 77

Query: 62  AGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAVA 121
              +DTQVNGGGG++ NH PT   +  + Q H Q+GT A+LPTVI+D++ VM+ A D   
Sbjct: 78  PALVDTQVNGGGGVLINHQPTAAGINTLTQTHGQYGTGALLPTVISDNLAVMEQALDGAI 137

Query: 122 EAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQ--DLGVRLITLAP 179
            A       ++GIHFEGPHLS+AK+GCH PA +R I E E  LY      LG  ++TLAP
Sbjct: 138 AARQGGDAAVVGIHFEGPHLSLAKKGCHSPALIRPIGEAEMTLYADAVAALGCCMVTLAP 197

Query: 180 ESVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVG 239
           E+V P  I RLVA G  +SLGHSNAD  TV  ++ AGASGFTHL+NGMSAL  REPGMVG
Sbjct: 198 ETVEPADIARLVALGVRVSLGHSNADVATVEASLAAGASGFTHLFNGMSALQGREPGMVG 257

Query: 240 AAFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKV 299
           AA A    YCGIILDG+HVH  SA  AWR KGT  LMLVTDAMSP G+ +  F+FF GKV
Sbjct: 258 AALACPEAYCGIILDGEHVHATSATLAWRLKGTRRLMLVTDAMSPTGTREESFEFFGGKV 317

Query: 300 VREGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIA 359
            R+GM LRD+ GSLAGSVL M +AVR A   L +  + A+ MAT TPA F+    +G +A
Sbjct: 318 HRDGMVLRDEQGSLAGSVLTMTAAVRQACAMLGVSAAEALWMATATPAAFLGLKDIGRLA 377

Query: 360 EGKQADWVWLDDDQRVLAVWIAGELL 385
            G +AD + LDD    L  W AG+L+
Sbjct: 378 PGNRADLLLLDDALYQLGRWQAGQLV 403


Lambda     K      H
   0.320    0.134    0.400 

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: 497
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: 394
Length of database: 411
Length adjustment: 31
Effective length of query: 363
Effective length of database: 380
Effective search space:   137940
Effective search space used:   137940
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 6937024 Sama_1198 (N-acetylglucosamine-6-phosphate deacetylase (RefSeq))
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.9542.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.1e-77  246.5   0.0    2.8e-77  246.2   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937024  Sama_1198 N-acetylglucosamine-6-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937024  Sama_1198 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.2   0.0   2.8e-77   2.8e-77      25     368 ..      50     389 ..      34     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 2.8e-77
                         TIGR00221  25 vindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etleimsealaksGvtsfLptlit 100
                                        i ++ i++++ +   + +  +  l+g +l+p l+D q+nG+gGv +n + +   ++ + ++  ++G+ + Lpt+i+
  lcl|FitnessBrowser__SB2B:6937024  50 KISQGHIETISRRP--DVDLPQYRLPG-ILAPALVDTQVNGGGGVLINHQPTaAGINTLTQTHGQYGTGALLPTVIS 123
                                       56666666665333..33344445555.89******************9877699********************** PP

                         TIGR00221 101 redeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdv.itkvtlapee 176
                                        +   +++a+  a+++    ++  ++G+h+eGP+lsl kkG h +  ir++  + +  + d+ + +   +vtlape 
  lcl|FitnessBrowser__SB2B:6937024 124 DNLAVMEQALDGAIAARQGGDA-AVVGIHFEGPHLSLAKKGCHSPALIRPIGEAEMTLYADAVAALgCCMVTLAPET 199
                                       ***********99998876665.9**************************987776888888776526789****77 PP

                         TIGR00221 177 kqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlh 253
                                        ++a++  +l+  g+ vs+Gh+na++++++++  aG++  thl+n ms l++Repg++Ga+L+  + +++ii DG h
  lcl|FitnessBrowser__SB2B:6937024 200 VEPADI-ARLVALGVRVSLGHSNADVATVEASLAAGASGFTHLFNGMSALQGREPGMVGAALACPEAYCGIILDGEH 275
                                       777775.568999**************************************************************** PP

                         TIGR00221 254 ihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveis 330
                                       +h + + la +lkg  +l+lvtD++++ g++ e+f+f G +v   +  l d++g laGs+ltm  +v+++    ++s
  lcl|FitnessBrowser__SB2B:6937024 276 VHATSATLAWRLKGTRRLMLVTDAMSPTGTREESFEFFGGKVHRDGMVLRDEQGSLAGSVLTMTAAVRQACAMLGVS 352
                                       ******************************************999999999************************** PP

                         TIGR00221 331 lsdvvrisslnparalgiddrlGsvakGkdanLavltk 368
                                        ++++ +++  pa  lg++d  G +a G  a+L +l+ 
  lcl|FitnessBrowser__SB2B:6937024 353 AAEALWMATATPAAFLGLKDI-GRLAPGNRADLLLLDD 389
                                       *******************98.***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (411 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: 11.62
//
[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