Alignments for a candidate for gcvT in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Escherichia coli BW25113

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 16985 b2905 glycine cleavage system aminomethyltransferase T (NCBI)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__Keio:16985
          Length = 364

 Score =  731 bits (1888), Expect = 0.0
 Identities = 364/364 (100%), Positives = 364/364 (100%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS
Sbjct: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK
Sbjct: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG
Sbjct: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM
Sbjct: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF
Sbjct: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG
Sbjct: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360

Query: 361 KAVA 364
           KAVA
Sbjct: 361 KAVA 364


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: 658
Number of extensions: 15
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 16985 b2905 (glycine cleavage system aminomethyltransferase T (NCBI))
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.31752.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.8e-175  566.6   0.0   1.1e-174  566.5   0.0    1.0  1  lcl|FitnessBrowser__Keio:16985  b2905 glycine cleavage system am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16985  b2905 glycine cleavage system aminomethyltransferase T (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.5   0.0  1.1e-174  1.1e-174       1     362 []       2     359 ..       2     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 566.5 bits;  conditional E-value: 1.1e-174
                       TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk. 78 
                                     +++tpLy++ht +g+++vdf+Gw++P++y+s+i+eh+avrt+aG+fDvshm++v+l+Gs++++fL++llanDv++Ltk 
  lcl|FitnessBrowser__Keio:16985   2 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKs 80 
                                     68****************************************************************************9 PP

                       TIGR00528  79 GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kakt 153
                                     Gka+ys++lna+GGv+DDlivy+++ed +f+lvvn+at+ekDl+w+++h+e++++++t+++++s++a+qGP    ka+t
  lcl|FitnessBrowser__Keio:16985  81 GKALYSGMLNASGGVIDDLIVYYFTED-FFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPnaqaKAAT 158
                                     ***************************.*******************************************999999** PP

                       TIGR00528 154 iledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrlea 232
                                     +++d++++aveg+k+ff+vq+++l     +ia+tGytGe+G+eia++neka+++w++lvea gvkP+GLgarDtLrlea
  lcl|FitnessBrowser__Keio:16985 159 LFNDAQRQAVEGMKPFFGVQAGDL-----FIATTGYTGEAGYEIALPNEKAADFWRALVEA-GVKPCGLGARDTLRLEA 231
                                     ************************.....********************************.***************** PP

                       TIGR00528 233 gmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..ngekev 309
                                     gm+LyGqe+de+i+Pl+a++gw++++e++++dfiGr++le+q+e+gtek lvGl+m+ekg++rnel+v++t  +g++++
  lcl|FitnessBrowser__Keio:16985 232 GMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEK-LVGLVMTEKGVLRNELPVRFTdaQGNQHE 309
                                     ************************************************9.********************98889**** PP

                       TIGR00528 310 GivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                     Gi+tsGt+sPtLg++iala+v+   e+iG++++v++rn+++++kv+k++fvr+
  lcl|FitnessBrowser__Keio:16985 310 GIITSGTFSPTLGYSIALARVP---EGIGETAIVQIRNREMPVKVTKPVFVRN 359
                                     **********************...99************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.68
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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