Alignments for a candidate for gcvT in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Dyella japonica UNC79MFTsu3.2

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate N515DRAFT_4331 N515DRAFT_4331 aminomethyltransferase

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4331
          Length = 366

 Score =  402 bits (1033), Expect = e-117
 Identities = 214/367 (58%), Positives = 260/367 (70%), Gaps = 12/367 (3%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M ++T L   H   GARMVDF GW MP++YGSQI+EHHAVR DAGMFDVSHMT+VDL G 
Sbjct: 1   MTEKTVLNATHRALGARMVDFGGWDMPINYGSQIEEHHAVRQDAGMFDVSHMTVVDLHGE 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           RTREFLR+LLAN+V KL   GKALYS ML+  GGVIDDLIVY+F +  FRLVVN+ATR K
Sbjct: 61  RTREFLRHLLANNVDKLKAQGKALYSCMLDEQGGVIDDLIVYFFDDRHFRLVVNAATRAK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFF----- 175
           DL+WI Q A+ FG+E+  R D SMIAVQGPNA+ K   L ++  R+ +  +  F      
Sbjct: 121 DLAWIEQQAKAFGVEVKERPDFSMIAVQGPNARDKVIGLLHEVDRERIRKLGKFVAAAAQ 180

Query: 176 GVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNL 235
           G     LFIA TGYTGE G+EI +P E A   W AL+ AGVKP GLGARDTLRLEAGMNL
Sbjct: 181 GPHGMPLFIARTGYTGEDGFEIIVPEEHAVALWEALLAAGVKPAGLGARDTLRLEAGMNL 240

Query: 236 YGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEK-LVGLVMTEKGVLRN 294
           YGQ+MDET+SP  AN+GWTI+ +   RDFIGR+ LE Q+  G ++ +VGLV+ EKGVLR+
Sbjct: 241 YGQDMDETVSPWEANLGWTISLDEG-RDFIGRKVLEAQKAAGVKRVMVGLVLDEKGVLRH 299

Query: 295 ELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKP 354
              V   +      EG I SG+F+PTL  ++A AR+P G      V IR RE+PV+V K 
Sbjct: 300 GQKVLTANG-----EGEILSGSFAPTLNKAVAFARIPAGEPGEVRVDIRGREVPVRVVKY 354

Query: 355 VFVRNGK 361
            FVR+GK
Sbjct: 355 PFVRDGK 361


Lambda     K      H
   0.320    0.136    0.402 

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: 472
Number of extensions: 20
Number of successful extensions: 5
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: 364
Length of database: 366
Length adjustment: 30
Effective length of query: 334
Effective length of database: 336
Effective search space:   112224
Effective search space used:   112224
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 N515DRAFT_4331 N515DRAFT_4331 (aminomethyltransferase)
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.7626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.3e-133  431.3   0.0   1.5e-133  431.1   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331  N515DRAFT_4331 aminomethyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4331  N515DRAFT_4331 aminomethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.1   0.0  1.5e-133  1.5e-133       2     361 ..       3     358 ..       2     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 431.1 bits;  conditional E-value: 1.5e-133
                                    TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqr 67 
                                                  ++t L   h  lg+++vdf+Gw +P++y+s+ieeh+avr++aG+fDvshm+ v+l G+++++fL++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331   3 EKTVLNATHRALGARMVDFGGWDMPINYGSQIEEHHAVRQDAGMFDVSHMTVVDLHGERTREFLRH 68 
                                                  689999************************************************************ PP

                                    TIGR00528  68 llanDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeev 132
                                                  llan+vd+L   Gka+ys +l  qGGv+DDlivy + +  +f+lvvnaat+ kDl+w++++++ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331  69 LLANNVDKLKAqGKALYSCMLDEQGGVIDDLIVYFFDDR-HFRLVVNAATRAKDLAWIEQQAKAFG 133
                                                  *********988**********************98777.************************** PP

                                    TIGR00528 133 tldtlskeisllalqGPkakt....iledlldkaveglkefffvqeaelalkkaliartGytGedG 194
                                                   + + + + s++a+qGP+a++    +l+++ ++ + +l +f+   ++   +   +iartGytGedG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331 134 VEVKERPDFSMIAVQGPNARDkvigLLHEVDRERIRKLGKFVAAAAQGPHGMPLFIARTGYTGEDG 199
                                                  *****************7765433367777777777777777776666666667************ PP

                                    TIGR00528 195 feiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker 260
                                                  fei+v++e+av lw++l++a gvkP GLgarDtLrleagm+LyGq++de+++P ea+lgw+++++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331 200 FEIIVPEEHAVALWEALLAA-GVKPAGLGARDTLRLEAGMNLYGQDMDETVSPWEANLGWTISLD- 263
                                                  ********************.********************************************. PP

                                    TIGR00528 261 kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknia 326
                                                  + +dfiGr+vle qk+ g+++ +vGl++ ekg++r++ kvl++ng   +G + sG+++PtL+k++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331 264 EGRDFIGRKVLEAQKAAGVKRVMVGLVLDEKGVLRHGQKVLTANG---EGEILSGSFAPTLNKAVA 326
                                                  9*****************************************999...9***************** PP

                                    TIGR00528 327 layvdkelekiGtklevevrnklvkikvvkklfvr 361
                                                   a+++   ++   ++ v++r+++v+++vvk +fvr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4331 327 FARIP---AGEPGEVRVDIRGREVPVRVVKYPFVR 358
                                                  *****...4555579******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (366 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: 7.63
//
[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