Aligments for a candidate for gcvT in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Aligments for a candidate for gcvT in Bacteroides thetaiotaomicron VPI-5482

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 354110 BT4584 putative aminomethyltransferase (NCBI ptt file)

Query= curated2:B2RI74
         (362 letters)



>lcl|FitnessBrowser__Btheta:354110 BT4584 putative
           aminomethyltransferase (NCBI ptt file)
          Length = 361

 Score =  521 bits (1341), Expect = e-152
 Identities = 256/362 (70%), Positives = 294/362 (81%), Gaps = 1/362 (0%)

Query: 1   MKTTPFTDVHIALGAKMHEFAGYNMPIEYGGIIDEHMNVVNNVGVFDVSHMGEFWVKGPN 60
           MKTTPFT+ HIALGAKMHEFAGYNMPIEY GIIDEH+ V N VGVFDVSHMGEFWVKGP 
Sbjct: 1   MKTTPFTEKHIALGAKMHEFAGYNMPIEYSGIIDEHLTVCNAVGVFDVSHMGEFWVKGPQ 60

Query: 61  ALRFLQKVSSNDASKLAVGQVQYCCFPNNDGGIVDDFLLYRYEEEKYMMVPNAANIAKDW 120
           AL FLQKV+SN+ + L  G++QY CFPN +GGIVDD L+Y YE EKY++V NAANI KDW
Sbjct: 61  ALAFLQKVTSNNVAALVPGKIQYTCFPNEEGGIVDDLLVYCYEPEKYLLVVNAANIEKDW 120

Query: 121 AWCRQQNTMGAILENASDNIAQLAVQGPKATEVMQRLTDIDLNEITYYTFKVGSFAGCPD 180
            WC   NT GA LEN+SDN+AQLAVQGPKA   +Q+LTDIDL+ I YYTF VG FAG  +
Sbjct: 121 NWCVSHNTEGAELENSSDNMAQLAVQGPKAILALQKLTDIDLSAIPYYTFTVGRFAGKEN 180

Query: 181 VIISATGYTGAGGFELYFYPQYAQKIWDALFEAGKPEGIKPAGLGARDTLRLEMGFCLYG 240
           VIIS TGYTGAGGFELYFYP  A+ IW A+FEAG+  GIKP GLGARDTLRLEMGFCLYG
Sbjct: 181 VIISNTGYTGAGGFELYFYPDAAEAIWKAVFEAGEEFGIKPVGLGARDTLRLEMGFCLYG 240

Query: 241 NDICDTTSPIEAGLGWITKFTDDKMDMPSRKIMEEQKAGGLKRKLVAFELKDKGIPRQHY 300
           ND+ D TSPIEAGLGWITKF + K +  +R ++E+QK+ G  RKLV FE+ D+GIPR  Y
Sbjct: 241 NDLDDKTSPIEAGLGWITKFVEGK-EFINRPMLEKQKSEGTTRKLVGFEMIDRGIPRHGY 299

Query: 301 EIANAEGQIIGEVTSGTMSPCLKKGIGMGYVATEFSKVGTELGIMVRGRQLKAEIVKPPF 360
           E+ N EG+ IG VTSGTMSP  K GIGMGYV  E++KVGTE+ I +RGR+LKA +VKPPF
Sbjct: 300 ELVNEEGEGIGVVTSGTMSPTRKIGIGMGYVKPEYAKVGTEICIDMRGRKLKAIVVKPPF 359

Query: 361 RK 362
           RK
Sbjct: 360 RK 361


Lambda     K      H
   0.320    0.138    0.420 

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: 506
Number of extensions: 20
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: 362
Length of database: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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: 49 (23.5 bits)

Align candidate 354110 BT4584 (putative aminomethyltransferase (NCBI ptt file))
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# 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/TIGR00528.hmm
# target sequence database:        /tmp/gapView.28389.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.5e-122  393.4   0.0   5.1e-122  393.2   0.0    1.0  1  lcl|FitnessBrowser__Btheta:354110  BT4584 putative aminomethyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:354110  BT4584 putative aminomethyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.2   0.0  5.1e-122  5.1e-122       2     360 ..       2     360 ..       1     361 [] 0.98

  Alignments for each domain:
  == domain 1  score: 393.2 bits;  conditional E-value: 5.1e-122
                          TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLt 77 
                                        k tp+ + h  lg+k+ +faG+++P++y+++i+eh  v +++G+fDvshmg++ ++G+++l+fLq++++n+v+aL 
  lcl|FitnessBrowser__Btheta:354110   2 KTTPFTEKHIALGAKMHEFAGYNMPIEYSGIIDEHLTVCNAVGVFDVSHMGEFWVKGPQALAFLQKVTSNNVAALV 77 
                                        789************************************************************************* PP

                          TIGR00528  78 kGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkakt 153
                                        +Gk qy+ + n +GG+vDDl+vy  + + ++llvvnaa++ekD +w   h +e+++l++ s++++ la+qGPka  
  lcl|FitnessBrowser__Btheta:354110  78 PGKIQYTCFPNEEGGIVDDLLVYCYEPE-KYLLVVNAANIEKDWNWCVSHNTEGAELENSSDNMAQLAVQGPKAIL 152
                                        ***********************99888.9********************************************** PP

                          TIGR00528 154 iledlldkaveglkefffvqeaelalkka.liartGytGedGfeiavanekavelwkklvea...ygvkPiGLgar 225
                                         l++l+d ++++++ ++f   + +a+k+  +i+ tGytG  Gfe++  ++ a  +wk++ ea   +g+kP+GLgar
  lcl|FitnessBrowser__Btheta:354110 153 ALQKLTDIDLSAIPYYTFT-VGRFAGKENvIISNTGYTGAGGFELYFYPDAAEAIWKAVFEAgeeFGIKPVGLGAR 227
                                        ***************9999.889998887699***************************9988889********** PP

                          TIGR00528 226 DtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvl 301
                                        DtLrle g +LyG++ld++++P+eaglgw+ k   + ++fi r +le+qk +gt +klvG+em+++gi+r++++++
  lcl|FitnessBrowser__Btheta:354110 228 DTLRLEMGFCLYGNDLDDKTSPIEAGLGWITKFV-EGKEFINRPMLEKQKSEGTTRKLVGFEMIDRGIPRHGYELV 302
                                        ******************************9999.999************************************** PP

                          TIGR00528 302 ltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfv 360
                                          +g + +G+vtsGt+sPt ++ i+++yv+ e++k+Gt++ +++r++++k+ vvk++f 
  lcl|FitnessBrowser__Btheta:354110 303 NEEG-EGIGVVTSGTMSPTRKIGIGMGYVKPEYAKVGTEICIDMRGRKLKAIVVKPPFR 360
                                        *999.99*************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (361 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.93
//
[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 preprint on GapMind for carbon sources, or view the source code.

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