Alignments for a candidate for manA in Bacillus safensis FO-36b

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Bacillus safensis FO-36b

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_034281142.1 BA81_RS05925 mannose-6-phosphate isomerase, class I

Query= BRENDA::A4ITT1
         (320 letters)



>NCBI__GCF_000691165.1:WP_034281142.1
          Length = 316

 Score =  429 bits (1102), Expect = e-125
 Identities = 201/314 (64%), Positives = 238/314 (75%)

Query: 1   MHQEPIFLTPVFQERIWGGTKLAERFGYDIPSSQTGECWAVSAHPHGQTVVARGPFQGMT 60
           M Q PIFL P  +ERIWGGT L ++FGYDIPS QTGECWA+SAHP+G +VV  GP++G T
Sbjct: 1   MKQSPIFLLPELKERIWGGTALRDQFGYDIPSDQTGECWAISAHPNGPSVVQDGPYKGKT 60

Query: 61  LGQLWEERRDLFGNFPSDRFPLLTKILDANADLSVQVHPDDDYAKTNEGGELGKTECWYI 120
           L +LW+  R+LFG    DRFPLLTKILDAN DLSVQVHPDDDYA+ +E GELGKTECWYI
Sbjct: 61  LIELWDNHRELFGGIEGDRFPLLTKILDANQDLSVQVHPDDDYAERHENGELGKTECWYI 120

Query: 121 IDCKPGAQLIYGHYAQTKEELRAMMEAGEWDRLLRKVPIHPGDFFYVPSGTIHALCEGTL 180
           IDCK GA++IYGH A+T+ EL  MM +G+W+ LLR+V I PGDF+YVPSGTIHALCEGTL
Sbjct: 121 IDCKEGAEMIYGHNARTRTELVTMMNSGDWEGLLRRVKIKPGDFYYVPSGTIHALCEGTL 180

Query: 181 VLETQQSSDTTYRVYDYDRVDSQGRKRELHLEKAIDVTTVPHRDTDVQPHVANIPGATVT 240
           VLETQQSSDTTYRVYDY+R D  G +RELH  +AIDVTTVPH D      V    G T+ 
Sbjct: 181 VLETQQSSDTTYRVYDYERKDQDGNERELHFAQAIDVTTVPHVDGYADESVETRRGVTIR 240

Query: 241 TFVEGDYFGVQKWHVHGEAEWEQTKPFLIVSILQGEGELVHGERTYPIRQGDHFILPHQF 300
           TFVE +YF V KW +  +AE  Q  PFL+ S++ GEG L H   TYP+ +G HFILP + 
Sbjct: 241 TFVEAEYFSVYKWEIDQKAELSQDYPFLLCSVIHGEGSLEHDGHTYPLPKGAHFILPAET 300

Query: 301 GRFAIRGTLEAIAS 314
           G F+I G+ E I S
Sbjct: 301 GSFSIEGSCELIVS 314


Lambda     K      H
   0.320    0.138    0.441 

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: 466
Number of extensions: 18
Number of successful extensions: 1
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: 320
Length of database: 316
Length adjustment: 27
Effective length of query: 293
Effective length of database: 289
Effective search space:    84677
Effective search space used:    84677
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: 48 (23.1 bits)

Align candidate WP_034281142.1 BA81_RS05925 (mannose-6-phosphate isomerase, class I)
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))

# 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/TIGR00218.hmm
# target sequence database:        /tmp/gapView.1636476.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00218  [M=359]
Accession:   TIGR00218
Description: manA: mannose-6-phosphate isomerase, class I
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-99  320.0   0.0    2.7e-62  196.9   0.0    2.0  2  NCBI__GCF_000691165.1:WP_034281142.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691165.1:WP_034281142.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   0.0   5.1e-40   5.1e-40       4     104 ..       6     104 ..       3     106 .. 0.95
   2 !  196.9   0.0   2.7e-62   2.7e-62     142     359 .]     102     315 ..     101     315 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 5.1e-40
                             TIGR00218   4 lfrvqknlkerdWGkgtaladllgysipskqtaElWag.aHkkgsSkvqng..kkvsLrdliekhksellGka 73 
                                           +f + + lker+WG gtal+d +gy ips qt+E+Wa+ aH++g+S vq g  k+++L++l+++h+ el+G  
  NCBI__GCF_000691165.1:WP_034281142.1   6 IFLLPE-LKERIWG-GTALRDQFGYDIPSDQTGECWAIsAHPNGPSVVQDGpyKGKTLIELWDNHR-ELFGGI 75 
                                           667777.99*****.***********************************999*************.****** PP

                             TIGR00218  74 eadrfelPlLvkvLsaekplsiqvHPdkala 104
                                           e+dr  +PlL+k+L+a+++ls+qvHPd + a
  NCBI__GCF_000691165.1:WP_034281142.1  76 EGDR--FPLLTKILDANQDLSVQVHPDDDYA 104
                                           ****..*********************8776 PP

  == domain 2  score: 196.9 bits;  conditional E-value: 2.7e-62
                             TIGR00218 142 riaelheeaerlgkteawviiasdekikeaaeilkealknskeelkekiqrliypedvglfkgllLnrvklkp 214
                                           ++ae he++e lgkte+w+ii+++e     ae+++++++++++el+++       ++ g+++ +lL+rvk+kp
  NCBI__GCF_000691165.1:WP_034281142.1 102 DYAERHENGE-LGKTECWYIIDCKE----GAEMIYGHNARTRTELVTMM------NS-GDWE-GLLRRVKIKP 161
                                           79********.**************....********************......66.****.********** PP

                             TIGR00218 215 geaiyvrsgtvHAy.kggdvlEvmanSdnvvragltd........kyldvkklvevltveekpeeklkeqkqk 278
                                           g+++yv+sgt+HA+ +g++vlE+++ Sd+++r+++++        ++l++++++ v tv++++ + +++ +++
  NCBI__GCF_000691165.1:WP_034281142.1 162 GDFYYVPSGTIHALcEGTLVLETQQSSDTTYRVYDYErkdqdgneRELHFAQAIDVTTVPHVDGYADESVETR 234
                                           **************9********************************************************** PP

                             TIGR00218 279 egaevlflvpieefavlktdlsekaelksqdsalillvleGdglilsgekklklkkGesfliaakleevtieg 351
                                           +g+++ ++v+ e+f+v+k+++++kael ++ ++l+++v++G+g + +++++++l kG +f+++a+++++ ieg
  NCBI__GCF_000691165.1:WP_034281142.1 235 RGVTIRTFVEAEYFSVYKWEIDQKAELSQDYPFLLCSVIHGEGSLEHDGHTYPLPKGAHFILPAETGSFSIEG 307
                                           ************************************************************************* PP

                             TIGR00218 352 edealvsv 359
                                            +e +vs+
  NCBI__GCF_000691165.1:WP_034281142.1 308 SCELIVSH 315
                                           ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (316 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: 00:00:00.00
# Mc/sec: 11.66
//
[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