Alignments for a candidate for gcvT in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Shewanella oneidensis MR-1

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 199965 SO0779 glycine cleavage system T protein (NCBI ptt file)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__MR1:199965
          Length = 364

 Score =  510 bits (1313), Expect = e-149
 Identities = 247/361 (68%), Positives = 297/361 (82%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MA +T L+ +H    A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+
Sbjct: 1   MANKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGT 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
               FLR LLANDVAKL   GKALY GML+ + G+IDDLI YY T+ F+R+VVNSATREK
Sbjct: 61  DACAFLRKLLANDVAKLKVPGKALYGGMLDDNAGIIDDLITYYLTDTFYRVVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+WI + ++ F + +T R +L+MIAVQGPNA+AKAA +F+  Q  A+EGMKPFFG QAG
Sbjct: 121 DLAWIAKQSQGFDVTVTERPELAMIAVQGPNAKAKAAAVFSSEQNAAIEGMKPFFGKQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGEAGYEI +P  +A   W+AL++ GVKPCGLGARDTLRLEAGMNLYG +M
Sbjct: 181 SLFIATTGYTGEAGYEIIVPETEAEALWQALLDQGVKPCGLGARDTLRLEAGMNLYGLDM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DETI+PLAANMGWTIAWEP DRDFIGR+ALE  R+ GT+KLVGLVM EKGVLR+++PV F
Sbjct: 241 DETINPLAANMGWTIAWEPTDRDFIGRKALEALRDAGTDKLVGLVMEEKGVLRHDMPVFF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDA G + +G+ITSGTFSPTLGYSIA+ARVP  IG+TA V++R + + V+V  P FVRNG
Sbjct: 301 TDAAGVEQQGVITSGTFSPTLGYSIAMARVPSSIGDTAEVEMRKKRVAVRVVAPNFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 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: 484
Number of extensions: 12
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 199965 SO0779 (glycine cleavage system T protein (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.13443.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     5e-141  455.8   0.1   5.6e-141  455.6   0.1    1.0  1  lcl|FitnessBrowser__MR1:199965  SO0779 glycine cleavage system T


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199965  SO0779 glycine cleavage system T protein (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.6   0.1  5.6e-141  5.6e-141       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 455.6 bits;  conditional E-value: 5.6e-141
                       TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk.G 79 
                                     ++t L++ h e  +k+vdf+Gw +P++y+s+ieeh+avr++aG+fDvshm+ v+++G+++ +fL++llanDv++L + G
  lcl|FitnessBrowser__MR1:199965   3 NKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGTDACAFLRKLLANDVAKLKVpG 81 
                                     79*************************************************************************988* PP

                       TIGR00528  80 kaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kakti 154
                                     ka+y ++l  + G++DDli y+ ++  ++++vvn+at+ekDl+w+ ++ +++    t + e++++a+qGP    ka+++
  lcl|FitnessBrowser__MR1:199965  82 KALYGGMLDDNAGIIDDLITYYLTDT-FYRVVVNSATREKDLAWIAKQSQGFDVTVTERPELAMIAVQGPnakaKAAAV 159
                                     ************************99.*******************************************99999999* PP

                       TIGR00528 155 ledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleag 233
                                     +   +++a+eg+k+ff+ q++ l     +ia+tGytGe+G+ei+v++ +a  lw++l+++ gvkP+GLgarDtLrleag
  lcl|FitnessBrowser__MR1:199965 160 FSSEQNAAIEGMKPFFGKQAGSL-----FIATTGYTGEAGYEIIVPETEAEALWQALLDQ-GVKPCGLGARDTLRLEAG 232
                                     ***********************.....********************************.****************** PP

                       TIGR00528 234 maLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..ngekevG 310
                                     m+LyG ++de+i Pl+a++gw++++e++++dfiGr++le  ++ gt+k lvGl+m ekg++r++++v++t   g ++ G
  lcl|FitnessBrowser__MR1:199965 233 MNLYGLDMDETINPLAANMGWTIAWEPTDRDFIGRKALEALRDAGTDK-LVGLVMEEKGVLRHDMPVFFTdaAGVEQQG 310
                                     **********************************************99.*********************4446799** PP

                       TIGR00528 311 ivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                     ++tsGt+sPtLg++ia+a+v+   + iG+++eve+r+k v ++vv + fvr+
  lcl|FitnessBrowser__MR1:199965 311 VITSGTFSPTLGYSIAMARVP---SSIGDTAEVEMRKKRVAVRVVAPNFVRN 359
                                     *********************...99***********************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.98
//
[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