Alignments for a candidate for manA in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Lactobacillus shenzhenensis LY-73

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_040535326.1 L248_RS06580 mannose-6-phosphate isomerase, class I

Query= BRENDA::A4ITT1
         (320 letters)



>NCBI__GCF_000469325.1:WP_040535326.1
          Length = 324

 Score =  340 bits (871), Expect = 4e-98
 Identities = 168/318 (52%), Positives = 219/318 (68%), Gaps = 6/318 (1%)

Query: 4   EPIFLTPVFQERIWGGTKLAERFGYDIPSSQTGECWAVSAHPHGQTVVARGPFQGMTLGQ 63
           EP+FL P FQ +IWGG KLA  FGY IP  + GECWA+SAHPHG + V  GP  G+ L  
Sbjct: 4   EPLFLHPYFQPKIWGGRKLASEFGYKIPDGKIGECWAISAHPHGPSRVINGPLAGLALDD 63

Query: 64  LWEERRDLFGNFPSDRFPLLTKILDANADLSVQVHPDDDYAKTNEGGELGKTECWYIIDC 123
            ++   + FG+     FPLLTKILDA A LSVQVHPDD YA+ +E  ELGKTECWY+I  
Sbjct: 64  AYKLHPEYFGDPSEKVFPLLTKILDAEASLSVQVHPDDAYAEEHEH-ELGKTECWYVIQA 122

Query: 124 KPGAQLIYGHYAQTKEELRAMMEAGEWDRLLRKVPIHPGDFFYVPSGTIHALCEGTLVLE 183
            PG+ LIYGH+AQT++EL  M+ AGEWD+LLRKVP+  GDF +VPSGTIHAL +G +VLE
Sbjct: 123 DPGSYLIYGHHAQTRQELADMIHAGEWDKLLRKVPVKTGDFIFVPSGTIHALNKGIMVLE 182

Query: 184 TQQSSDTTYRVYDYDRVDSQ-GRKRELHLEKAIDVTTVPHRDTDVQPHVANIPGATVTTF 242
           TQQSSDTTYR+YDYDRVD++ G+KR+LHL+++IDVT VPH D  +         +T TT+
Sbjct: 183 TQQSSDTTYRLYDYDRVDAKTGKKRDLHLQQSIDVTNVPHHDPKLDIQTEQRGASTFTTY 242

Query: 243 VE---GDYFGVQKWHVHG-EAEWEQTKPFLIVSILQGEGELVHGERTYPIRQGDHFILPH 298
           V+     +F V +W +   +A    + P+ +VS+L G+G L      Y + +G HFI+P 
Sbjct: 243 VQPPISPFFSVWQWRIKDKQALHHVSAPYTLVSVLAGDGTLTADGDPYELHKGMHFIIPA 302

Query: 299 QFGRFAIRGTLEAIASWP 316
           Q   + + G ++ IAS P
Sbjct: 303 QIKDWTVDGDMQIIASEP 320


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: 428
Number of extensions: 22
Number of successful extensions: 4
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: 324
Length adjustment: 28
Effective length of query: 292
Effective length of database: 296
Effective search space:    86432
Effective search space used:    86432
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_040535326.1 L248_RS06580 (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.1978933.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-71  227.9   0.0      4e-44  137.2   0.0    2.0  2  NCBI__GCF_000469325.1:WP_040535326.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_040535326.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   6.7e-30   6.7e-30       7     104 ..      11     104 ..       5     107 .. 0.92
   2 !  137.2   0.0     4e-44     4e-44     144     357 ..     104     317 ..     101     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 6.7e-30
                             TIGR00218   7 vqknlkerdWGkgtaladllgysipskqtaElWag.aHkkgsSkvqng..kkvsLrdliekhksellGkaead 76 
                                            ++    ++WG g +la  +gy+ip  +++E+Wa+ aH++g+S+v ng  ++  L+d ++ h+ e +G   ++
  NCBI__GCF_000469325.1:WP_040535326.1  11 YFQ---PKIWG-GRKLASEFGYKIPDGKIGECWAIsAHPHGPSRVINGplAGLALDDAYKLHP-EYFGDPSEK 78 
                                           444...89***.***********************************99**************.********* PP

                             TIGR00218  77 rfelPlLvkvLsaekplsiqvHPdkala 104
                                           +  +PlL+k+L+ae  ls+qvHPd a a
  NCBI__GCF_000469325.1:WP_040535326.1  79 V--FPLLTKILDAEASLSVQVHPDDAYA 104
                                           *..*********************6665 PP

  == domain 2  score: 137.2 bits;  conditional E-value: 4e-44
                             TIGR00218 144 aelheeaerlgkteawviiasdekikeaaeilkealknskeelkekiqrliypedvglfkgllLnrvklkpge 216
                                           ae h e e lgkte+w++i+ d        +++++++++++el  +i        +g+++  lL++v +k g+
  NCBI__GCF_000469325.1:WP_040535326.1 104 AEEH-EHE-LGKTECWYVIQADP----GSYLIYGHHAQTRQELADMI------H-AGEWD-KLLRKVPVKTGD 162
                                           4443.345.**************....999*****************......5.5****.************ PP

                             TIGR00218 217 aiyvrsgtvHAy.kggdvlEvmanSdnvvragltd.........kyldvkklvevltveekpeeklkeqkqke 279
                                           +i+v+sgt+HA+ kg+ vlE+++ Sd+++r++++d         + l++++++ v +v++++ + + +++q+ 
  NCBI__GCF_000469325.1:WP_040535326.1 163 FIFVPSGTIHALnKGIMVLETQQSSDTTYRLYDYDrvdaktgkkRDLHLQQSIDVTNVPHHDPKLDIQTEQRG 235
                                           ************99*****************************99**************99988777777776 PP

                             TIGR00218 280 ..gaevlflvpiee.favlktdlsekaelksqd.salillvleGdglilsgekklklkkGesfliaakleevt 348
                                               ++ +++pi   f+v ++ +++k +l+++  ++ +++vl Gdg++ +++  ++l+kG +f+i+a++++ t
  NCBI__GCF_000469325.1:WP_040535326.1 236 asTFTTYVQPPISPfFSVWQWRIKDKQALHHVSaPYTLVSVLAGDGTLTADGDPYELHKGMHFIIPAQIKDWT 308
                                           2233344455665438***********988775167899********************************** PP

                             TIGR00218 349 iegedealv 357
                                           ++g+ + ++
  NCBI__GCF_000469325.1:WP_040535326.1 309 VDGDMQIIA 317
                                           ****88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (324 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: 6.27
//
[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